probably bug in the `lung_lobe_segmentation_workflow.py`

[kayhan-batmanghelich]

Hi,

I am trying to use the develop version to compute the lung partial volume mask. When I use lung_lobe_segmentation_workflow.py, it first complained that the cip (and a few other things) were not defined. I noticed that a few lines were commented out in the code. Is there any reason for that?

It seems it has issues with gprob. I added the teem-build/bin and CIP-build/bin to the PATH. Am I missing something?

Thanks,

170206-14:42:47,85 workflow INFO:
     ['check', 'execution', 'logging']
170206-14:42:47,115 workflow INFO:
     Running serially.
170206-14:42:47,116 workflow INFO:
     Executing node generate_partial_lung_label_map in dir: /tmp/tmp1JwoPq/LungLobeSegmentationWorkflow/generate_partial_lung_label_map
170206-14:42:47,124 workflow INFO:
     Running:  GeneratePartialLungLabelMap  --ict /home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resample_simpleMask/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz --olm /tmp/tmpMmsd0b/cid_partialLungLabelMap.nrrd
170206-14:42:48,444 interface INFO:
     stdout 2017-02-06T14:42:48.444537:Clipping low CT image values...
170206-14:42:48,445 interface INFO:
     stdout 2017-02-06T14:42:48.444537:Clipping upper CT image values...
170206-14:42:48,445 interface INFO:
     stdout 2017-02-06T14:42:48.444537:Executing partial lung filter...
170206-14:43:06,901 interface INFO:
     stdout 2017-02-06T14:43:06.900896:Writing lung mask image...
170206-14:43:07,402 interface INFO:
     stdout 2017-02-06T14:43:07.402132:DONE.
170206-14:43:07,931 workflow INFO:
     Executing node fissure_particles_node in dir: /tmp/tmpuqJIBf/LungLobeSegmentationWorkflow/fissure_particles_node
unu 3op: error parsing "/home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resample_simpleMask/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz" as nrrd/value for <in2> option:
[nrrd] nrrdLoad: trouble reading "/home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resample_simpleMask/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: couldn't parse "e0;'@ c" as magic or beginning of any recognized format

Usage: unu 3op <operator> <in1> <in2> <in3> [-t,--type <type>] \
       [-w,--which <arg>] [-o,--output <nout>]

<operator> = Ternary operator. Possibilities include:
             o "+", "x": sum or product of three values
             o "min", "max": minimum, maximum
             o "min_sm": smoothed minimum function; min_sm(x, w, M) is like
             min(x,M) but for x > M-w (with w > 0) there is a smooth
             transition from x to asymptotic to M
             o "max_sm": smoothed maximum function; max_sm(M, w, x) is like
             max(M,x) but for x < m+w (with w > m) there is a smooth
             transition from x to asymptotic to m
             o "lt_sm": 1st less than 3rd, smoothed by 2nd
             o "gt_sm": 1st greater than 3rd, smoothed by 2nd
             o "clamp": 2nd value is clamped to range between the 1st and
             the 3rd
             o "ifelse": if 1st value non-zero, then 2nd value, else 3rd
             value
             o "lerp": linear interpolation between the 2nd and 3rd values,
             as the 1st value varies between 0.0 and 1.0, respectively
             o "exists": if the 1st value exists, use the 2nd value,
             otherwise use the 3rd
             o "in_op": 1 iff 2nd value is > 1st and < 3rd, 0 otherwise
             o "in_cl": 1 iff 2nd value is >= 1st and <= 3rd, 0 otherwise
             o "gauss": evaluate (at 1st value) Gaussian with mean=2nd and
             stdv=3rd value
             o "rician": evaluate (at 1st value) Rician with mean=2nd and
             stdv=3rd value
     <in1> = First input. Can be a single value or a nrrd.
     <in2> = Second input. Can be a single value or a nrrd.
     <in3> = Third input. Can be a single value or a nrrd.
 -t <type> , --type <type> = type to convert all nrrd inputs to, prior to
             doing operation. This also determines output type. By default
             (not using this option), the types of the input nrrds are left
             unchanged.
  -w <arg> , --which <arg> = Which argument (0, 1, or 2) should be used to
             determine the shape of the output nrrd. By default (not using
             this option), the first non-constant argument is used. (int);
             default: "-1"
 -o <nout> , --output <nout> = output nrrd (string); default: "-"
unu resample: error parsing "-" as nrrd for -i,--input option:
[nrrd] nrrdLoad: trouble reading "-"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: immediately hit EOF

Usage: unu resample [-old] -s,--size <sz0 ...> [-off,--offset [<off0 ...>]] \
       [-min,--minimum [<min0 ...>]] [-max,--maximum [<max0 ...>]] \
       [-k,--kernel <kern>] [-nrn] [-ne,--nonexistent <behavior>] \
       [-b,--boundary <behavior>] [-v,--value <value>] [-t,--type <type>] \
       [-cheap] [-c,--center <center>] [-co,--center-override] [-verbose <v>] \
       [-i,--input <nin>] [-o,--output <nout>]

             -old = instead of using the new nrrdResampleContext
                    implementation, use the old nrrdSpatialResample
                    implementation
     -s <sz0 ...> , --size <sz0 ...> = For each axis, information about how
                    many samples in output:
                    o "=": leave this axis completely untouched: no
                    resampling whatsoever
                    o "x<float>": multiply the number of input samples by
                    <float>, and round to the nearest integer, to get the
                    number of output samples. Use "x1" to resample the axis
                    but leave the number of samples unchanged
                    o "/<float>": divide number of samples by <float>
                    o "+=<uint>", "-=<uint>": add <uint> to or subtract
                    <uint> from number input samples to get number output
                    samples
                    o "<uint>": exact number of output samples
                    o "a": resample this axis to whatever number of samples
                    preserves the aspect ratio of other resampled axes.
                    Currently needs to be used on all but one of the resampled
                    axes, if at all. 
                    (1 or more sampling specifications)
-off [<off0 ...>] , --offset [<off0 ...>] = For each axis, an offset or shift
                    to the position (in index space) of the lower end of the
                    sampling domain. Either -off can be used, or -min and -max
                    together, or none of these (so that, by default, the full
                    domain of the axis is resampled). (0 or more doubles);
                    default: ""
-min [<min0 ...>] , --minimum [<min0 ...>] = For each axis, the lower end (in
                    index space) of the domain of the resampling. Either -off
                    can be used, or -min and -max together, or none of these
                    (so that, by default, the full domain of the axis is
                    resampled). (0 or more doubles); default: ""
-max [<max0 ...>] , --maximum [<max0 ...>] = For each axis, the upper end (in
                    index space) of the domain of the resampling. Either -off
                    can be used, or -min and -max together, or none of these,
                    so that (by default), the full domain of the axis is
                    resampled. (0 or more doubles); default: ""
        -k <kern> , --kernel <kern> = The kernel to use for resampling.
                    Kernels logically live in the input index space for
                    upsampling, and in the output index space for
                    downsampling. Possibilities include:
                    o "box": nearest neighbor interpolation on upsampling,
                    and uniform averaging on downsampling
                    o "cheap": nearest neighbor interpolation for
                    upsampling, and non-blurring sub-sampling (pick subset of
                    input samples) on downsampling
                    o "tent": linear interpolation
                    o "cubic:B,C": Mitchell/Netravali BC-family of cubics:
                      "cubic:1,0": B-spline; maximal blurring
                      "cubic:0,0.5": Catmull-Rom; good interpolating kernel
                    o "c4h": 6-sample-support, C^4 continuous, accurate
                    o "c4hai": discrete pre-filter to make c4h interpolate
                    o "bspl3", "bspl5", "bspl7": cubic (same as cubic:1,0),
                    quintic, and 7th order B-spline
                    o "bspl3ai", "bspl5ai", "bspl7ai": discrete pre-filters
                    to make bspl3, bspl5, bspl7 interpolate
                    o "hann:R": Hann (cosine bell) windowed sinc, radius R
                    o "black:R": Blackman windowed sinc, radius R
                    o "gauss:S,C": Gaussian blurring, with standard
                    deviation S and cut-off at C standard deviations
                    o "dgauss:S,C": Lindeberg's discrete Gaussian.
                    default: "cubic:0,0.5"
             -nrn = do NOT do per-pass kernel weight renormalization. Doing
                    the renormalization is not a performance hit (hence is
                    enabled by default), and the renormalization is sometimes
                    needed to avoid "grating" on non-integral down-sampling.
                    Disabling the renormalization is needed for correct
                    results with artificially narrow kernels.
   -ne <behavior> , --nonexistent <behavior> = When resampling floating-point
                    values, how to handle non-existent values within kernel
                    support:
                    o "noop": do nothing; let them pollute result
                    o "renorm": ignore them and renormalize weights of
                    existent values
                    o "wght": ignore them and simply use weights of
                    existent values
                    default: "noop"
    -b <behavior> , --boundary <behavior> = How to handle samples beyond the
                    input bounds:
                    o "pad": use some specified value
                    o "bleed": extend border values outward
                    o "mirror": repeated reflections
                    o "wrap": wrap-around to other side
                    default: "bleed"
       -v <value> , --value <value> = for "pad" boundary behavior, pad with
                    this value (double); default: "0.0"
        -t <type> , --type <type> = type to save OUTPUT as. By default (not
                    using this option), the output type is the same as the
                    input type; default: "default"
           -cheap = [DEPRECATED: the "-k cheap" option is the new (and more
                    reliable) way to access this functionality. "-cheap" is
                    only here for legacy use in combination with "-old".]
                    When downsampling (reducing number of samples), don't try
                    to do correct filtering by scaling kernel to match new
                    (stretched) index space; keep it in old index space. When
                    used in conjunction with "-k box", this can implement
                    subsampling which chooses every Nth value.
      -c <center> , --center <center> = (not available with "-old") default
                    centering of axes when input nrrd axes don't have a known
                    centering: "cell" or "node" ; default: "cell"
              -co , --center-override = (not available with "-old") centering
                    info specified via "-c" should *over-ride* known
                    centering, rather than simply be used when centering is
                    unknown.
     -verbose <v> = (not available with "-old") verbosity level (int);
                    default: "0"
         -i <nin> , --input <nin> = input nrrd; default: "-"
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
unu resample: error parsing "/home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resample_simpleMask/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz" as nrrd for -i,--input option:
[nrrd] nrrdLoad: trouble reading "/home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resample_simpleMask/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: couldn't parse "e0;'@ c" as magic or beginning of any recognized format

Usage: unu resample [-old] -s,--size <sz0 ...> [-off,--offset [<off0 ...>]] \
       [-min,--minimum [<min0 ...>]] [-max,--maximum [<max0 ...>]] \
       [-k,--kernel <kern>] [-nrn] [-ne,--nonexistent <behavior>] \
       [-b,--boundary <behavior>] [-v,--value <value>] [-t,--type <type>] \
       [-cheap] [-c,--center <center>] [-co,--center-override] [-verbose <v>] \
       [-i,--input <nin>] [-o,--output <nout>]

             -old = instead of using the new nrrdResampleContext
                    implementation, use the old nrrdSpatialResample
                    implementation
     -s <sz0 ...> , --size <sz0 ...> = For each axis, information about how
                    many samples in output:
                    o "=": leave this axis completely untouched: no
                    resampling whatsoever
                    o "x<float>": multiply the number of input samples by
                    <float>, and round to the nearest integer, to get the
                    number of output samples. Use "x1" to resample the axis
                    but leave the number of samples unchanged
                    o "/<float>": divide number of samples by <float>
                    o "+=<uint>", "-=<uint>": add <uint> to or subtract
                    <uint> from number input samples to get number output
                    samples
                    o "<uint>": exact number of output samples
                    o "a": resample this axis to whatever number of samples
                    preserves the aspect ratio of other resampled axes.
                    Currently needs to be used on all but one of the resampled
                    axes, if at all. 
                    (1 or more sampling specifications)
-off [<off0 ...>] , --offset [<off0 ...>] = For each axis, an offset or shift
                    to the position (in index space) of the lower end of the
                    sampling domain. Either -off can be used, or -min and -max
                    together, or none of these (so that, by default, the full
                    domain of the axis is resampled). (0 or more doubles);
                    default: ""
-min [<min0 ...>] , --minimum [<min0 ...>] = For each axis, the lower end (in
                    index space) of the domain of the resampling. Either -off
                    can be used, or -min and -max together, or none of these
                    (so that, by default, the full domain of the axis is
                    resampled). (0 or more doubles); default: ""
-max [<max0 ...>] , --maximum [<max0 ...>] = For each axis, the upper end (in
                    index space) of the domain of the resampling. Either -off
                    can be used, or -min and -max together, or none of these,
                    so that (by default), the full domain of the axis is
                    resampled. (0 or more doubles); default: ""
        -k <kern> , --kernel <kern> = The kernel to use for resampling.
                    Kernels logically live in the input index space for
                    upsampling, and in the output index space for
                    downsampling. Possibilities include:
                    o "box": nearest neighbor interpolation on upsampling,
                    and uniform averaging on downsampling
                    o "cheap": nearest neighbor interpolation for
                    upsampling, and non-blurring sub-sampling (pick subset of
                    input samples) on downsampling
                    o "tent": linear interpolation
                    o "cubic:B,C": Mitchell/Netravali BC-family of cubics:
                      "cubic:1,0": B-spline; maximal blurring
                      "cubic:0,0.5": Catmull-Rom; good interpolating kernel
                    o "c4h": 6-sample-support, C^4 continuous, accurate
                    o "c4hai": discrete pre-filter to make c4h interpolate
                    o "bspl3", "bspl5", "bspl7": cubic (same as cubic:1,0),
                    quintic, and 7th order B-spline
                    o "bspl3ai", "bspl5ai", "bspl7ai": discrete pre-filters
                    to make bspl3, bspl5, bspl7 interpolate
                    o "hann:R": Hann (cosine bell) windowed sinc, radius R
                    o "black:R": Blackman windowed sinc, radius R
                    o "gauss:S,C": Gaussian blurring, with standard
                    deviation S and cut-off at C standard deviations
                    o "dgauss:S,C": Lindeberg's discrete Gaussian.
                    default: "cubic:0,0.5"
             -nrn = do NOT do per-pass kernel weight renormalization. Doing
                    the renormalization is not a performance hit (hence is
                    enabled by default), and the renormalization is sometimes
                    needed to avoid "grating" on non-integral down-sampling.
                    Disabling the renormalization is needed for correct
                    results with artificially narrow kernels.
   -ne <behavior> , --nonexistent <behavior> = When resampling floating-point
                    values, how to handle non-existent values within kernel
                    support:
                    o "noop": do nothing; let them pollute result
                    o "renorm": ignore them and renormalize weights of
                    existent values
                    o "wght": ignore them and simply use weights of
                    existent values
                    default: "noop"
    -b <behavior> , --boundary <behavior> = How to handle samples beyond the
                    input bounds:
                    o "pad": use some specified value
                    o "bleed": extend border values outward
                    o "mirror": repeated reflections
                    o "wrap": wrap-around to other side
                    default: "bleed"
       -v <value> , --value <value> = for "pad" boundary behavior, pad with
                    this value (double); default: "0.0"
        -t <type> , --type <type> = type to save OUTPUT as. By default (not
                    using this option), the output type is the same as the
                    input type; default: "default"
           -cheap = [DEPRECATED: the "-k cheap" option is the new (and more
                    reliable) way to access this functionality. "-cheap" is
                    only here for legacy use in combination with "-old".]
                    When downsampling (reducing number of samples), don't try
                    to do correct filtering by scaling kernel to match new
                    (stretched) index space; keep it in old index space. When
                    used in conjunction with "-k box", this can implement
                    subsampling which chooses every Nth value.
      -c <center> , --center <center> = (not available with "-old") default
                    centering of axes when input nrrd axes don't have a known
                    centering: "cell" or "node" ; default: "cell"
              -co , --center-override = (not available with "-old") centering
                    info specified via "-c" should *over-ride* known
                    centering, rather than simply be used when centering is
                    unknown.
     -verbose <v> = (not available with "-old") verbosity level (int);
                    default: "0"
         -i <nin> , --input <nin> = input nrrd; default: "-"
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
puller: trouble with volumes or infos:
[meet] meetPullVolLoadMulti: trouble loading mpv[0]->nin ("V")
[meet] [nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz","rb") failed: No such file or directory
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
unu 2op: error parsing "-" as nrrd/value for <in1> option:
[nrrd] nrrdLoad: trouble reading "-"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: immediately hit EOF

Usage: unu 2op <operator> <in1> <in2> [-s,--seed <seed>] [-t,--type <type>] \
       [-w,--which <arg>] [-o,--output <nout>]

<operator> = Binary operator. Possibilities include:
             o "+", "-", "x", "/": add, subtract, multiply, divide
             o "^": exponentiation (pow)
             o "spow": signed exponentiation: sgn(x)pow(abs(x),p)
             o "fpow": like spow but with curves flipped
             o "%": integer modulo
             o "fmod": same as fmod() in C
             o "atan2": same as atan2() in C
             o "min", "max": minimum, maximum
             o "lt", "lte", "gt", "gte": same as C's <, <=, >, <=
             o "eq", "neq": same as C's == and !=
             o "comp": -1, 0, or 1 if 1st value is less than, equal to, or
             greater than 2nd value
             o "if": if 1st value is non-zero, use it, else use 2nd value
             o "exists": if 1st value exists, use it, else use 2nd value
             o "nrand": scale unit-stdv Gaussian noise by 2nd value and add
             to first value
             o "rrand": sample Rician distribution with 1st value for
             "true" mean, and 2nd value for sigma
     <in1> = First input. Can be a single value or a nrrd.
     <in2> = Second input. Can be a single value or a nrrd.
 -s <seed> , --seed <seed> = seed value for RNG for nrand, so that you can
             get repeatable results between runs, or, by not using this
             option, the RNG seeding will be based on the current time
             (string)
 -t <type> , --type <type> = type to convert all INPUT nrrds to, prior to
             doing operation, useful for doing, for instance, the difference
             between two unsigned char nrrds. This will also determine output
             type. By default (not using this option), the types of the input
             nrrds are left unchanged.
  -w <arg> , --which <arg> = Which argument (0 or 1) should be used to
             determine the shape of the output nrrd. By default (not using
             this option), the first non-constant argument is used. (int);
             default: "-1"
 -o <nout> , --output <nout> = output nrrd (string); default: "-"
unu inset: error parsing "-" as nrrd for -s,--subset option:
[nrrd] nrrdLoad: trouble reading "-"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: immediately hit EOF

Usage: unu inset -min,--minimum <pos0 ...> -s,--subset <nsub> \
       [-i,--input <nin>] [-o,--output <nout>]

-min <pos0 ...> , --minimum <pos0 ...> = coordinates of where to locate
                  sub-volume within input nrrd.
                  o <int> gives 0-based index
                  o M, M+<int>, M-<int> give index relative to the last
                  sample on the axis (M == #samples-1).
                  (1 or more positions)
      -s <nsub> , --subset <nsub> = sub-region nrrd. This the data to be
                  inset in "nin"
       -i <nin> , --input <nin> = input nrrd
      -o <nout> , --output <nout> = output nrrd (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
unu crop: error parsing "/tmp/tmpF_O60K/pass3.nrrd" as nrrd for -i,--input option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/pass3.nrrd","rb") failed: No such file or directory

Usage: unu crop [-min,--minimum [<pos0 ...>]] [-max,--maximum [<pos0 ...>]] \
       [-b,--bounds <filename>] [-i,--input <nin>] [-o,--output <nout>]

-min [<pos0 ...>] , --minimum [<pos0 ...>] = low corner of bounding box.
                    o <int> gives 0-based index
                    o M, M+<int>, M-<int> give index relative to the last
                    sample on the axis (M == #samples-1).
                    (0 or more positions)
                    default: "0"
-max [<pos0 ...>] , --maximum [<pos0 ...>] = high corner of bounding box.
                    Besides the specification styles described above, there's
                    also:
                    o m+<int> give index relative to minimum.
                    (0 or more positions)
                    default: "0"
    -b <filename> , --bounds <filename> = a filename given here overrides the
                    -min and -max options (they don't need to be used) and
                    provides the cropping bounds as a 2-D array; first
                    scanline is for -min, second is for -max. Unfortunately
                    the "m" and "M" semantics (above) are currently not
                    supported in the bounds file.
         -i <nin> , --input <nin> = input nrrd
        -o <nout> , --output <nout> = output nrrd (string); default: "-"
ERROR: error parsing "/tmp/tmpF_O60K/ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("/tmp/tmpF_O60K/ct-deconv.nrrd","rb") failed: No such file or directory

Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
       gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
       [-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
       range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
       [-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
       sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
       [-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]

                  -i <nin> = input volume
                 -k <kind> = "kind" of volume ("scalar", "vector", "tensor",
                             or "dwi")
            -v <verbosity> = verbosity level (int); default: "1"
                -q <query> = the quantity (scalar, vector, or matrix) to learn
                             by probing (string)
        -gmc <min gradmag> = For curvature-based queries, use zero when
                             gradient magnitude is below this (double);
                             default: "0.0"
                      -ofs = If only per-axis spacing is available, use that
                             to contrive full orientation info
                 -seed <N> = RNG seed; mostly for debugging (unsigned int);
                             default: "42"
                 -c <bool> = clamp positions as part of probing (bool);
                             default: "false"
                -zz <bool> = enable "zeroZ" behavior in gage that partially
                             implements working with 3D images as if they are
                             2D (bool); default: "false"
             -k00 <kern00> = kernel for gageKernel00; default: "tent"
             -k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
             -k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
                       -rn = renormalize kernel weights at each new sample
                             location. "Accurate" kernels don't need this;
                             doing it always makes things go slower
               -ssn <SS #> = how many scale-space samples to evaluate, or, 0
                             to turn-off all scale-space behavior (unsigned
                             int); default: "0"
        -ssr <scale range> = range of scales in scale-space (2 doubles);
                             default: "nan nan"
                      -ssu = do uniform samples along sigma, and not (by
                             default) samples according to the effective
                             diffusion scale
                      -sso = if not using "-ssu", use pre-computed optimal
                             sigmas when possible
            -kssb <kernel> = blurring kernel, to sample scale space;
                             default: "dgauss:1,5"
          -sbp <blur spec> = complete specification of stack blur parms;
                             over-rides all previous "ss" options; default: ""
                     -ssnd = normalize derivatives by scale
              -ssnb <bias> = bias on scale-based derivative normalization
                             (double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
                             filenames from which to read pre-blurred volumes
                             computed for the stack, if they exist and match
                             the stack parameters, and where to save them if
                             they had to be re-computed. Leave this as empty
                             string to disable this. (string); default: ""
            -kssr <kernel> = kernel for reconstructing from scale space
                             samples; default: "hermite"
       -s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
                             : supersampling); use "-ssp" (and "-psi")to
                             specify scale position of sampling (3 doubles);
                             default: "1 1 1"
                -ssp <pos> = when using scale-space, scale-position at which
                             to probe (double); default: "0"
                -pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
                             and direction vectors for sampling grid;
                             default: ""
                -pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
                             4-vec positions; default: ""
             -pp <pos ...> = overrides "-pi": only sample at this specified
                             point (3..4 doubles); default: "nan nan nan"
            -eps <epsilon> = if non-zero, and if query is a scalar, and if
                             using "pp" to query at a single point, then do
                             epsilon offset probes to calculate discrete
                             differences, to find the numerical gradient and
                             hessian (for debugging) (double); default: "0"
                  -psi <p> = whether the probe location specification (by any
                             of the four previous flags) are in index space
                             (bool); default: "false"
                 -t <type> = type of output volume (type); default: "float"
                 -o <nout> = output volume (string); default: "-"
170206-14:43:08,594 workflow ERROR:
     ['Node fissure_particles_node failed to run on host r001.pvt.bridges.psc.edu.']
170206-14:43:08,596 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-144308-batmangh-fissure_particles_node-8d99b1a9-0f3e-4d91-b674-4b7fcc953c1b.pklz
170206-14:43:08,596 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1000, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/interfaces/cip/cip_python_interfaces.py", line 56, in _run_interface
    dp.execute()
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/fissure_particles.py", line 129, in execute
    self.save_vtk(out_particles % 3)
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/chest_particles.py", line 566, in save_vtk
    im=image_io.read(self._sp_in_file_name)
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/input_output/image_reader_writer.py", line 29, in read
    sitk_image=sitk.ReadImage(file_name)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 8450, in ReadImage
    return _SimpleITK.ReadImage(*args)
RuntimeError: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageReaderBase.cxx:76:
sitk::ERROR: The file "/tmp/tmpF_O60K/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz" does not exist.
Interface fissure_particles failed to run. 

170206-14:43:08,616 workflow INFO:
     Executing node generate_lobe_surface_models in dir: /tmp/tmp8E5ImE/LungLobeSegmentationWorkflow/generate_lobe_surface_models
170206-14:43:08,622 workflow INFO:
     Running:  GenerateLobeSurfaceModels  --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpMmsd0b/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpMmsd0b/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpMmsd0b/cid_rightLungLobesShapeModel.csv
170206-14:43:09,407 interface INFO:
     stdout 2017-02-06T14:43:09.406861:Read in 100 atlas resource file pairs.
170206-14:43:09,407 interface INFO:
     stdout 2017-02-06T14:43:09.406861:Reading fixed image...
170206-14:43:09,908 interface INFO:
     stderr 2017-02-06T14:43:09.908129:
170206-14:43:09,908 interface INFO:
     stderr 2017-02-06T14:43:09.908129:CIP Assertion Error:
170206-14:43:09,908 interface INFO:
     stderr 2017-02-06T14:43:09.908129:In file: /home/batmangh/MyPylon1Space/gitSandbox/ChestImagingPlatform-dev/CommandLineTools/GenerateLobeSurfaceModels/GenerateLobeSurfaceModels.cxx
170206-14:43:09,909 interface INFO:
     stderr 2017-02-06T14:43:09.908129:On line: 111
170206-14:43:09,909 interface INFO:
     stderr 2017-02-06T14:43:09.908129:Aborting!
170206-14:43:10,412 workflow ERROR:
     ['Node generate_lobe_surface_models failed to run on host r001.pvt.bridges.psc.edu.']
170206-14:43:10,413 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-144310-batmangh-generate_lobe_surface_models-c4ff63c5-f9e7-4a0c-b2ee-b0e076d25b49.pklz
170206-14:43:10,413 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
    self.raise_exception(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
 GenerateLobeSurfaceModels  --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpMmsd0b/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpMmsd0b/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpMmsd0b/cid_rightLungLobesShapeModel.csv
Standard output:
Read in 100 atlas resource file pairs.
Reading fixed image...
Standard error:

CIP Assertion Error:
In file:    /home/batmangh/MyPylon1Space/gitSandbox/ChestImagingPlatform-dev/CommandLineTools/GenerateLobeSurfaceModels/GenerateLobeSurfaceModels.cxx
On line:    111
Aborting!
Return code: -6
Interface GenerateLobeSurfaceModels failed to run. 

170206-14:43:10,432 workflow INFO:
     ***********************************
170206-14:43:10,432 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.fissure_particles_node
170206-14:43:10,432 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-144308-batmangh-fissure_particles_node-8d99b1a9-0f3e-4d91-b674-4b7fcc953c1b.pklz
170206-14:43:10,432 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.generate_lobe_surface_models
170206-14:43:10,432 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-144310-batmangh-generate_lobe_surface_models-c4ff63c5-f9e7-4a0c-b2ee-b0e076d25b49.pklz
170206-14:43:10,432 workflow INFO:
     ***********************************
Traceback (most recent call last):
  File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow2.py", line 468, in <module>
    wf.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
    report_nodes_not_run(notrun)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[rjosest]

Hi Kayhan,

Great to hear from you and thanks for reporting this issues. We will look into this issues and we’ll let you know. Just as a quick check, the workflows assume that the CLI that are packed with CIP are in your path. The CLIs are installed under CIP-build/bin

Thanks

/R

On Feb 6, 2017, at 1:47 PM, Kayhan Batmanghelich notifications@github.com wrote:

Hi,

I am trying to use the develop version to compute the lung partial volume mask. When I use lung_lobe_segmentation_workflow.py, it first complained that the cip (and a few other things) were not defined. I noticed that a few lines were commented out in the code. Is there any reason for that?

When I uncomment it, it started working up to this point (see below). It sounds to me that it is trying to run GeneratePartialLungLabelMap.cxx which is a source code not the executable. I guess there is a bug but I cannot find it.

Could you please help to fix it?

Thanks,

170206-13:18:48,41 workflow INFO: ['check', 'execution', 'logging'] 170206-13:18:48,67 workflow INFO: Running serially. 170206-13:18:48,68 workflow INFO: Executing node generate_partial_lung_label_map in dir: /tmp/tmpoS0__i/LungLobeSegmentationWorkflow/generate_partial_lung_label_map 170206-13:18:48,76 workflow INFO: Running: GeneratePartialLungLabelMap --ict /home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resample_simpleMask/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz --olm /tmp/tmp8gse5e/cid_partialLungLabelMap.nrrd 170206-13:18:51,167 interface INFO: stdout 2017-02-06T13:18:51.166921:Clipping low CT image values... 170206-13:18:51,167 interface INFO: stdout 2017-02-06T13:18:51.166921:Clipping upper CT image values... 170206-13:18:51,676 interface INFO: stdout 2017-02-06T13:18:51.676826:Executing partial lung filter... 170206-13:19:07,576 interface INFO: stdout 2017-02-06T13:19:07.576830:Writing lung mask image... 170206-13:19:08,589 interface INFO: stdout 2017-02-06T13:19:08.589510:DONE. 170206-13:19:09,145 workflow INFO: Executing node generate_lobe_surface_models in dir: /tmp/tmpDJ78JX/LungLobeSegmentationWorkflow/generate_lobe_surface_models 170206-13:19:09,150 workflow INFO: Running: GenerateLobeSurfaceModels --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmp8gse5e/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmp8gse5e/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmp8gse5e/cid_rightLungLobesShapeModel.csv 170206-13:19:09,994 interface INFO: stdout 2017-02-06T13:19:09.994704:Read in 100 atlas resource file pairs. 170206-13:19:09,995 interface INFO: stdout 2017-02-06T13:19:09.994704:Reading fixed image... 170206-13:19:10,496 interface INFO: stderr 2017-02-06T13:19:10.495997: 170206-13:19:10,496 interface INFO: stderr 2017-02-06T13:19:10.495997:CIP Assertion Error: 170206-13:19:10,496 interface INFO: stderr 2017-02-06T13:19:10.495997:In file: /home/batmangh/MyPylon1Space/gitSandbox/ChestImagingPlatform-dev/CommandLineTools/GenerateLobeSurfaceModels/GenerateLobeSurfaceModels.cxx 170206-13:19:10,496 interface INFO: stderr 2017-02-06T13:19:10.495997:On line: 111 170206-13:19:10,496 interface INFO: stderr 2017-02-06T13:19:10.495997:Aborting! 170206-13:19:11,0 workflow ERROR: ['Node generate_lobe_surface_models failed to run on host r001.pvt.bridges.psc.edu.'] 170206-13:19:11,4 workflow INFO: Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-131911-batmangh-generate_lobe_surface_models-59c61ad1-49b3-4134-be1d-4d28958383f2.pklz 170206-13:19:11,4 workflow INFO: Traceback (most recent call last): File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run node.run(updatehash=updatehash) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run self._run_interface() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface self._result = self._run_command(execute) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command result = self._interface.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run runtime = self._run_wrapper(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper runtime = self._run_interface(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface self.raise_exception(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception raise RuntimeError(message) RuntimeError: Command: GenerateLobeSurfaceModels --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmp8gse5e/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmp8gse5e/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmp8gse5e/cid_rightLungLobesShapeModel.csv Standard output: Read in 100 atlas resource file pairs. Reading fixed image... Standard error:

CIP Assertion Error: In file: /home/batmangh/MyPylon1Space/gitSandbox/ChestImagingPlatform-dev/CommandLineTools/GenerateLobeSurfaceModels/GenerateLobeSurfaceModels.cxx On line: 111 Aborting! Return code: -6 Interface GenerateLobeSurfaceModels failed to run.

170206-13:19:11,25 workflow INFO: Executing node fissure_particles_node in dir: /tmp/tmptt1uIm/LungLobeSegmentationWorkflow/fissure_particles_node /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: puller: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found 170206-13:19:11,445 workflow ERROR: ['Node fissure_particles_node failed to run on host r001.pvt.bridges.psc.edu.'] 170206-13:19:11,446 workflow INFO: Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-131911-batmangh-fissure_particles_node-58cb3a08-8c71-4457-880c-8aa1de3e48eb.pklz 170206-13:19:11,446 workflow INFO: Traceback (most recent call last): File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run node.run(updatehash=updatehash) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run self._run_interface() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface self._result = self._run_command(execute) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command result = self._interface.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run runtime = self._run_wrapper(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1000, in _run_wrapper runtime = self._run_interface(runtime) File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/interfaces/cip/cip_python_interfaces.py", line 56, in _run_interface dp.execute() File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/fissure_particles.py", line 129, in execute self.save_vtk(out_particles % 3) File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/chest_particles.py", line 566, in save_vtk im=image_io.read(self._sp_in_file_name) File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/input_output/image_reader_writer.py", line 29, in read sitk_image=sitk.ReadImage(file_name) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 8450, in ReadImage return _SimpleITK.ReadImage(*args) RuntimeError: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageReaderBase.cxx:76: sitk::ERROR: The file "/tmp/tmpgcVTQ9/1.3.6.1.4.1.14519.5.2.1.6279.6001.100684836163890911914061745866resmpl1.0-1.0-1.0_lungMask.nii.gz" does not exist. Interface fissure_particles failed to run.

170206-13:19:11,455 workflow INFO:

---

170206-13:19:11,455 workflow ERROR: could not run node: LungLobeSegmentationWorkflow.generate_lobe_surface_models 170206-13:19:11,456 workflow INFO: crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-131911-batmangh-generate_lobe_surface_models-59c61ad1-49b3-4134-be1d-4d28958383f2.pklz 170206-13:19:11,456 workflow ERROR: could not run node: LungLobeSegmentationWorkflow.fissure_particles_node 170206-13:19:11,456 workflow INFO: crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-131911-batmangh-fissure_particles_node-58cb3a08-8c71-4457-880c-8aa1de3e48eb.pklz 170206-13:19:11,456 workflow INFO:

---

Traceback (most recent call last): File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow2.py", line 468, in wf.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run report_nodes_not_run(notrun) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/acil-bwh/ChestImagingPlatform/issues/14, or mute the thread https://github.com/notifications/unsubscribe-auth/ADD8kuwVv43TbLR39AyjHNCgsByq2YXAks5rZ2rBgaJpZM4L4khR.

[kayhan-batmanghelich]

Hi Raul,

Thank you for your reply. I had it in my path. It seems that it complains about gprob in the path (see below). When I add team-build/bin to my path, it complains about the unu stuff. Maybe interface to unu has changes?

170206-15:35:27,293 workflow INFO:
     ['check', 'execution', 'logging']
170206-15:35:27,323 workflow INFO:
     Running serially.
170206-15:35:27,324 workflow INFO:
     Executing node generate_partial_lung_label_map in dir: /tmp/tmpMrECas/LungLobeSegmentationWorkflow/generate_partial_lung_label_map
170206-15:35:27,331 workflow INFO:
     Running:  GeneratePartialLungLabelMap  --ict /home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resampled_subsets/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.970264865033574190975654369557resmpl1.0-1.0-1.0.mhd --olm /tmp/tmpMxE1m6/cid_pad
170206-15:35:28,613 interface INFO:
     stdout 2017-02-06T15:35:28.613538:Clipping low CT image values...
170206-15:35:28,613 interface INFO:
     stdout 2017-02-06T15:35:28.613538:Clipping upper CT image values...
170206-15:35:28,613 interface INFO:
     stdout 2017-02-06T15:35:28.613538:Executing partial lung filter...
170206-15:35:45,16 interface INFO:
     stdout 2017-02-06T15:35:45.016835:Writing lung mask image...
170206-15:35:45,518 interface INFO:
     stdout 2017-02-06T15:35:45.517893:DONE.
170206-15:35:46,47 workflow INFO:
     Executing node generate_lobe_surface_models in dir: /tmp/tmpoKGer6/LungLobeSegmentationWorkflow/generate_lobe_surface_models
170206-15:35:46,54 workflow INFO:
     Running:  GenerateLobeSurfaceModels  --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpMxE1m6/cid_partialLungLabelMap.nrrd --irlm /pylon1/msv
170206-15:35:46,837 interface INFO:
     stdout 2017-02-06T15:35:46.836861:Read in 100 atlas resource file pairs.
170206-15:35:46,837 interface INFO:
     stdout 2017-02-06T15:35:46.836861:Reading fixed image...
170206-15:35:47,340 interface INFO:
     stdout 2017-02-06T15:35:47.340832:Subsampling fixed image...
170206-15:35:47,341 interface INFO:
     stdout 2017-02-06T15:35:47.340832:Reading moving image...
170206-15:35:48,862 interface INFO:
     stdout 2017-02-06T15:35:48.862840:Subsampling moving image...
170206-15:35:48,863 interface INFO:
     stdout 2017-02-06T15:35:48.862840:Extracting whole lung region from down sampled fixed image...
170206-15:35:48,863 interface INFO:
     stdout 2017-02-06T15:35:48.862840:Extracting whole lung region from down sampled moving image...
170206-15:35:48,863 interface INFO:
     stdout 2017-02-06T15:35:48.862840:Registering reference image to input image...
170206-15:35:50,398 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading transform from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading fissure points from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading transform from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading fissure points from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading transform from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading fissure points from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading transform from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading fissure points from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading transform from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading fissure points from file...
170206-15:35:50,399 interface INFO:
     stdout 2017-02-06T15:35:50.398385:Reading transform from file...
170206-15:35:50,901 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,901 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,901 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,901 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,902 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,903 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,904 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,905 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,906 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,907 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,907 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,907 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,907 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,907 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,907 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,908 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,909 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,909 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
170206-15:35:50,909 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:50,909 interface INFO:
     stdout 2017-02-06T15:35:50.900632:Reading fissure points from file...
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     stdout 2017-02-06T15:35:50.900632:Reading transform from file...
170206-15:35:51,410 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
170206-15:35:51,411 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
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     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
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     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
170206-15:35:51,417 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
170206-15:35:51,417 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
170206-15:35:51,417 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
170206-15:35:51,418 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
170206-15:35:51,418 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
170206-15:35:51,418 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading transform from file...
170206-15:35:51,418 interface INFO:
     stdout 2017-02-06T15:35:51.409814:Reading fissure points from file...
170206-15:35:51,922 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,922 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,922 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,922 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading transform from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Reading fissure points from file...
170206-15:35:51,923 interface INFO:
     stdout 2017-02-06T15:35:51.922757:Getting range locations...
170206-15:35:53,962 interface INFO:
     stdout 2017-02-06T15:35:53.962052:Writing right shape model to file...
170206-15:35:53,962 interface INFO:
     stdout 2017-02-06T15:35:53.962052:Writing left shape model to file...
170206-15:35:53,962 interface INFO:
     stdout 2017-02-06T15:35:53.962052:DONE.
170206-15:35:54,492 workflow INFO:
     Executing node fissure_particles_node in dir: /tmp/tmpIzXGjJ/LungLobeSegmentationWorkflow/fissure_particles_node
/bin/sh: unu: command not found
/bin/sh: unu: command not found
/bin/sh: unu: command not found
/bin/sh: puller: command not found
/bin/sh: unu: command not found
/bin/sh: unu: command not found
/bin/sh: unu: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
/bin/sh: unu: command not found
/bin/sh: gprobe: command not found
170206-15:35:54,649 workflow ERROR:
     ['Node fissure_particles_node failed to run on host r001.pvt.bridges.psc.edu.']
170206-15:35:54,650 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-153554-batmangh-fissure_particles_node-50de00a4-73b6-4d62-9d69-6cc120fbd11b.pklz
170206-15:35:54,650 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1000, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/interfaces/cip/cip_python_interfaces.py", line 56, in _run_interface
    dp.execute()
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/fissure_particles.py", line 129, in execute
    self.save_vtk(out_particles % 3)
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/chest_particles.py", line 566, in save_vtk
    im=image_io.read(self._sp_in_file_name)
  File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/input_output/image_reader_writer.py", line 29, in read
    sitk_image=sitk.ReadImage(file_name)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 8450, in ReadImage
    return _SimpleITK.ReadImage(*args)
RuntimeError: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageReaderBase.cxx:76:
sitk::ERROR: The file "/tmp/tmpOE_CTx/1.3.6.1.4.1.14519.5.2.1.6279.6001.970264865033574190975654369557resmpl1.0-1.0-1.0.mhd" does not exist.
Interface fissure_particles failed to run.

170206-15:35:54,661 workflow INFO:
     ***********************************
170206-15:35:54,661 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.fissure_particles_node
170206-15:35:54,661 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-153554-batmangh-fissure_particles_node-50de00a4-73b6-4d62-9d69-6cc120fbd11b.pklz
170206-15:35:54,661 workflow INFO:
     ***********************************
Traceback (most recent call last):
  File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow2.py", line 468, in <module>
    wf.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
    report_nodes_not_run(notrun)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[jcross186]

Hi Kayhan,

Please do an update in the ‘develop’ branch and give it another shot. Let us know if you continue to have issues.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Monday, February 6, 2017 at 3:42 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi Raul,

Thank you for your reply. I had it in my path. It seems that it complains about gprob in the path (see below). When I add team-build/bin to my path, it complains about the unu stuff. Maybe interface to unu has changes?

170206-15:35:27,293 workflow INFO: ['check', 'execution', 'logging'] 170206-15:35:27,323 workflow INFO: Running serially. 170206-15:35:27,324 workflow INFO: Executing node generate_partial_lung_label_map in dir: /tmp/tmpMrECas/LungLobeSegmentationWorkflow/generate_partial_lung_label_map 170206-15:35:27,331 workflow INFO: Running: GeneratePartialLungLabelMap --ict /home/batmangh/MyPylon2Space/LUNA16/noduleSegmentation/resample_imgs/resampled_subsets/subset1/1.3.6.1.4.1.14519.5.2.1.6279.6001.970264865033574190975654369557resmpl1.0-1.0-1.0.mhd --olm /tmp/tmpMxE1m6/cid_pad 170206-15:35:28,613 interface INFO: stdout 2017-02-06T15:35:28.613538:Clipping low CT image values... 170206-15:35:28,613 interface INFO: stdout 2017-02-06T15:35:28.613538:Clipping upper CT image values... 170206-15:35:28,613 interface INFO: stdout 2017-02-06T15:35:28.613538:Executing partial lung filter... 170206-15:35:45,16 interface INFO: stdout 2017-02-06T15:35:45.016835:Writing lung mask image... 170206-15:35:45,518 interface INFO: stdout 2017-02-06T15:35:45.517893:DONE. 170206-15:35:46,47 workflow INFO: Executing node generate_lobe_surface_models in dir: /tmp/tmpoKGer6/LungLobeSegmentationWorkflow/generate_lobe_surface_models 170206-15:35:46,54 workflow INFO: Running: GenerateLobeSurfaceModels --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpMxE1m6/cid_partialLungLabelMap.nrrd --irlm /pylon1/msv 170206-15:35:46,837 interface INFO: stdout 2017-02-06T15:35:46.836861:Read in 100 atlas resource file pairs. 170206-15:35:46,837 interface INFO: stdout 2017-02-06T15:35:46.836861:Reading fixed image... 170206-15:35:47,340 interface INFO: stdout 2017-02-06T15:35:47.340832:Subsampling fixed image... 170206-15:35:47,341 interface INFO: stdout 2017-02-06T15:35:47.340832:Reading moving image... 170206-15:35:48,862 interface INFO: stdout 2017-02-06T15:35:48.862840:Subsampling moving image... 170206-15:35:48,863 interface INFO: stdout 2017-02-06T15:35:48.862840:Extracting whole lung region from down sampled fixed image... 170206-15:35:48,863 interface INFO: stdout 2017-02-06T15:35:48.862840:Extracting whole lung region from down sampled moving image... 170206-15:35:48,863 interface INFO: stdout 2017-02-06T15:35:48.862840:Registering reference image to input image... 170206-15:35:50,398 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading transform from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading fissure points from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading transform from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading fissure points from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading transform from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading fissure points from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading transform from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading fissure points from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading transform from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading fissure points from file... 170206-15:35:50,399 interface INFO: stdout 2017-02-06T15:35:50.398385:Reading transform from file... 170206-15:35:50,901 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,901 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,901 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,901 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,902 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,903 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,904 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,905 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,906 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,907 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,907 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,907 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,907 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,907 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,907 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,908 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,909 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,909 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,909 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:50,909 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading fissure points from file... 170206-15:35:50,909 interface INFO: stdout 2017-02-06T15:35:50.900632:Reading transform from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,410 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,411 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,412 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,413 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,414 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,415 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,416 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,417 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,418 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,418 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,418 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading transform from file... 170206-15:35:51,418 interface INFO: stdout 2017-02-06T15:35:51.409814:Reading fissure points from file... 170206-15:35:51,922 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,922 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,922 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,922 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading transform from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Reading fissure points from file... 170206-15:35:51,923 interface INFO: stdout 2017-02-06T15:35:51.922757:Getting range locations... 170206-15:35:53,962 interface INFO: stdout 2017-02-06T15:35:53.962052:Writing right shape model to file... 170206-15:35:53,962 interface INFO: stdout 2017-02-06T15:35:53.962052:Writing left shape model to file... 170206-15:35:53,962 interface INFO: stdout 2017-02-06T15:35:53.962052:DONE. 170206-15:35:54,492 workflow INFO: Executing node fissure_particles_node in dir: /tmp/tmpIzXGjJ/LungLobeSegmentationWorkflow/fissure_particles_node /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: puller: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found /bin/sh: unu: command not found /bin/sh: gprobe: command not found 170206-15:35:54,649 workflow ERROR: ['Node fissure_particles_node failed to run on host r001.pvt.bridges.psc.edu.'] 170206-15:35:54,650 workflow INFO: Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-153554-batmangh-fissure_particles_node-50de00a4-73b6-4d62-9d69-6cc120fbd11b.pklz 170206-15:35:54,650 workflow INFO: Traceback (most recent call last): File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run node.run(updatehash=updatehash) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run self._run_interface() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface self._result = self._run_command(execute) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command result = self._interface.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run runtime = self._run_wrapper(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1000, in _run_wrapper runtime = self._run_interface(runtime) File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/interfaces/cip/cip_python_interfaces.py", line 56, in _run_interface dp.execute() File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/fissure_particles.py", line 129, in execute self.save_vtk(out_particles % 3) File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/particles/chest_particles.py", line 566, in save_vtk im=image_io.read(self._sp_in_file_name) File "/pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/input_output/image_reader_writer.py", line 29, in read sitk_image=sitk.ReadImage(file_name) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 8450, in ReadImage return _SimpleITK.ReadImage(*args) RuntimeError: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageReaderBase.cxx:76: sitk::ERROR: The file "/tmp/tmpOE_CTx/1.3.6.1.4.1.14519.5.2.1.6279.6001.970264865033574190975654369557resmpl1.0-1.0-1.0.mhd" does not exist. Interface fissure_particles failed to run.

170206-15:35:54,661 workflow INFO:

---

170206-15:35:54,661 workflow ERROR: could not run node: LungLobeSegmentationWorkflow.fissure_particles_node 170206-15:35:54,661 workflow INFO: crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170206-153554-batmangh-fissure_particles_node-50de00a4-73b6-4d62-9d69-6cc120fbd11b.pklz 170206-15:35:54,661 workflow INFO:

---

Traceback (most recent call last): File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow2.py", line 468, in wf.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run report_nodes_not_run(notrun) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

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[kayhan-batmanghelich]

Hi James,

I pulled the develop version and rebuilt it. I still have the same issue. Not sure but it seems that in one of the steps it uses TEEM tools and it doesn't produce the results the rest of the pipeline expects; so it crashes. You can find the crash files here:

https://www.dropbox.com/s/xgbe7k8o1dzuofh/crash-20170209-165134-batmangh-fissure_particles_node-278f22bc-aaa5-4987-a2d0-8926143f0974.pklz?dl=0

I thought maybe my image is not good, so I applied on my of the COPDGene images. So it takes much longer. It produces different set of error, (see blow).

For my image, perhaps I should use different parameter since run time is very different? Is this pipeline appropriate for lowdose CT?

[batmangh@br006 CIP-build]$ python  cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py  --in_ct /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --out ~/test3.nrrd
170209-16:58:16,170 workflow INFO:
     ['check', 'execution', 'logging']
170209-16:58:16,190 workflow INFO:
     Running serially.
170209-16:58:16,190 workflow INFO:
     Executing node generate_partial_lung_label_map in dir: /tmp/tmpTieWJa/LungLobeSegmentationWorkflow/generate_partial_lung_label_map
170209-16:58:16,194 workflow INFO:
     Running:  GeneratePartialLungLabelMap  --ict /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --olm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd
170209-16:58:22,632 interface INFO:
     stdout 2017-02-09T16:58:22.632485:Clipping low CT image values...
170209-16:58:23,134 interface INFO:
     stdout 2017-02-09T16:58:23.134029:Clipping upper CT image values...
170209-16:58:23,635 interface INFO:
     stdout 2017-02-09T16:58:23.635879:Executing partial lung filter...
170209-17:00:37,928 interface INFO:
     stdout 2017-02-09T17:00:37.927810:Writing lung mask image...
170209-17:00:43,535 interface INFO:
     stdout 2017-02-09T17:00:43.535154:DONE.
170209-17:00:44,51 workflow INFO:
     Executing node fissure_particles_node in dir: /tmp/tmpqN4ZT2/LungLobeSegmentationWorkflow/fissure_particles_node
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     17: Hessian eigenvector[1]
gageQuerySet: expanded scalar query = ...
     17: Hessian eigenvector[1]
     15: Hessian eigenvectors
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     16: Hessian eigenvector[0]
gageQuerySet: expanded scalar query = ...
     16: Hessian eigenvector[0]
     15: Hessian eigenvectors
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
      1: value
gageQuerySet: expanded scalar query = ...
      1: value
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (1,0,0
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (1,0,0
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,0,0,0,0,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     18: Hessian eigenvector[2]
gageQuerySet: expanded scalar query = ...
     18: Hessian eigenvector[2]
     15: Hessian eigenvectors
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     12: Hessian eigenvalue[0]
gageQuerySet: expanded scalar query = ...
     12: Hessian eigenvalue[0]
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     13: Hessian eigenvalue[1]
gageQuerySet: expanded scalar query = ...
     13: Hessian eigenvalue[1]
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     14: Hessian eigenvalue[2]
gageQuerySet: expanded scalar query = ...
     14: Hessian eigenvalue[2]
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
      7: Hessian
gageQuerySet: expanded scalar query = ...
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     36: Hessian mode
gageQuerySet: expanded scalar query = ...
     36: Hessian mode
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
 -o /tmp/tmpVyCQgR/cid_fissureParticles.vtk -b -i /tmp/tmpuXoDMo/pass3.nrrd -a NA -i /tmp/tmpuXoDMo/hevec1.nrrd -a hevec1 -i /tmp/tmpuXoDMo/hevec0.nrrd -a hevec0 -i /tmp/tmpuXoDMo/val.nrrd -a val -i /tmp/tmpuXoDMo/hevec2.nrrd -a hevec2 -i /tmp/tmpuXoDMo/heval0.nrrd -a h0 -i /tmp/tmpuXoDMo/heval1.nrrd -a h1 -i /tmp/tmpuXoDMo/heval2.nrrd -a h2 -i /tmp/tmpuXoDMo/hess.nrrd -a hess -i /tmp/tmpuXoDMo/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.742188,0.742188,0.5 --cipr UndefinedRegion --cipt Fissure
Reading file for NA...
Reading file for hevec1...
Reading file for hevec0...
Reading file for val...
Reading file for hevec2...
Reading file for h0...
Reading file for h1...
Reading file for h2...
Reading file for hess...
Reading file for hmode...
Writing poly data...
DONE.
170209-17:24:07,676 workflow INFO:
     Runtime memory and threads stats unavailable
170209-17:24:07,679 workflow INFO:
     Executing node pre_filter_fissure_particle_data in dir: /tmp/tmpNISiDz/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data
170209-17:24:07,683 workflow INFO:
     Running:  FilterFissureParticleData  --dist 3.000000 --ifp /tmp/tmpVyCQgR/cid_fissureParticles.vtk --ofp /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --size 110
170209-17:24:08,443 interface INFO:
     stdout 2017-02-09T17:24:08.443405:Reading polydata...
170209-17:24:08,443 interface INFO:
     stdout 2017-02-09T17:24:08.443405:Filtering particles using connectedness...
170209-17:24:09,455 interface INFO:
     stdout 2017-02-09T17:24:09.455189:Writing filtered particles ...
170209-17:24:09,455 interface INFO:
     stdout 2017-02-09T17:24:09.455189:DONE.
170209-17:24:09,969 workflow INFO:
     Executing node extract_right_particles in dir: /tmp/tmpZYYFz3/LungLobeSegmentationWorkflow/extract_right_particles
170209-17:24:09,974 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr RightLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_rightPreFilteredFissureParticles.vtk
170209-17:24:10,710 interface INFO:
     stdout 2017-02-09T17:24:10.710154:Reading polydata...
170209-17:24:10,710 interface INFO:
     stdout 2017-02-09T17:24:10.710154:Reading label map...
170209-17:24:12,737 workflow ERROR:
     ['Node extract_right_particles failed to run on host br006.pvt.bridges.psc.edu.']
170209-17:24:12,739 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172412-batmangh-extract_right_particles-7074cdad-687e-4beb-aab9-e0e6c1bcd1ef.pklz
170209-17:24:12,739 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
    self.raise_exception(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
 ExtractParticlesFromChestRegionChestType  --cipr RightLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_rightPreFilteredFissureParticles.vtk
Standard output:
Reading polydata...
Reading label map...
Standard error:

Return code: -11
Interface ExtractParticlesFromChestRegionChestType failed to run.

170209-17:24:12,754 workflow INFO:
     Executing node generate_lobe_surface_models in dir: /tmp/tmpacLyHd/LungLobeSegmentationWorkflow/generate_lobe_surface_models
170209-17:24:12,759 workflow INFO:
     Running:  GenerateLobeSurfaceModels  --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpVyCQgR/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpVyCQgR/cid_rightLungLobesShapeModel.csv
170209-17:24:13,486 interface INFO:
     stdout 2017-02-09T17:24:13.486400:Read in 100 atlas resource file pairs.
170209-17:24:13,488 interface INFO:
     stdout 2017-02-09T17:24:13.486400:Reading fixed image...
170209-17:24:17,53 interface INFO:
     stdout 2017-02-09T17:24:17.052886:Subsampling fixed image...
170209-17:24:17,553 interface INFO:
     stdout 2017-02-09T17:24:17.553815:Reading moving image...
170209-17:24:18,565 interface INFO:
     stdout 2017-02-09T17:24:18.565348:Subsampling moving image...
170209-17:24:18,565 interface INFO:
     stdout 2017-02-09T17:24:18.565348:Extracting whole lung region from down sampled fixed image...
170209-17:24:18,565 interface INFO:
     stdout 2017-02-09T17:24:18.565348:Extracting whole lung region from down sampled moving image...
170209-17:24:18,565 interface INFO:
     stdout 2017-02-09T17:24:18.565348:Registering reference image to input image...
170209-17:24:27,747 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading transform from file...
170209-17:24:27,748 interface INFO:
     stdout 2017-02-09T17:24:27.747642:Reading fissure points from file...
170209-17:24:28,249 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,249 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,250 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,251 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,252 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading fissure points from file...
170209-17:24:28,252 interface INFO:
     stdout 2017-02-09T17:24:28.249522:Reading transform from file...
170209-17:24:28,753 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,753 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,753 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,753 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
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     stdout 2017-02-09T17:24:28.753375:Reading transform from file...
170209-17:24:28,754 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
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     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
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     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
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     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
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170209-17:24:28,755 interface INFO:
     stdout 2017-02-09T17:24:28.753375:Reading fissure points from file...
170209-17:24:29,256 interface INFO:
     stdout 2017-02-09T17:24:29.256075:Reading transform from file...
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     stdout 2017-02-09T17:24:29.256075:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.256075:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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170209-17:24:29,761 interface INFO:
     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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170209-17:24:29,762 interface INFO:
     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading fissure points from file...
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     stdout 2017-02-09T17:24:29.758518:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,263 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading transform from file...
170209-17:24:30,264 interface INFO:
     stdout 2017-02-09T17:24:30.263165:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
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     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,765 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,766 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,767 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,767 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,767 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading transform from file...
170209-17:24:30,767 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Reading fissure points from file...
170209-17:24:30,767 interface INFO:
     stdout 2017-02-09T17:24:30.765135:Getting range locations...
170209-17:24:32,799 interface INFO:
     stdout 2017-02-09T17:24:32.799802:Writing right shape model to file...
170209-17:24:32,800 interface INFO:
     stdout 2017-02-09T17:24:32.799802:Writing left shape model to file...
170209-17:24:32,800 interface INFO:
     stdout 2017-02-09T17:24:32.799802:DONE.
170209-17:24:33,317 workflow INFO:
     Executing node extract_left_particles in dir: /tmp/tmpt69OT0/LungLobeSegmentationWorkflow/extract_left_particles
170209-17:24:33,322 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr LeftLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_leftPreFilteredFissureParticles.vtk
170209-17:24:34,11 interface INFO:
     stdout 2017-02-09T17:24:34.011733:Reading polydata...
170209-17:24:34,12 interface INFO:
     stdout 2017-02-09T17:24:34.011733:Reading label map...
170209-17:24:36,36 workflow ERROR:
     ['Node extract_left_particles failed to run on host br006.pvt.bridges.psc.edu.']
170209-17:24:36,37 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172436-batmangh-extract_left_particles-76dca266-4bb1-4d0a-ad58-1ebb86c0decb.pklz
170209-17:24:36,37 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
    self.raise_exception(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
 ExtractParticlesFromChestRegionChestType  --cipr LeftLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_leftPreFilteredFissureParticles.vtk
Standard output:
Reading polydata...
Reading label map...
Standard error:

Return code: -11
Interface ExtractParticlesFromChestRegionChestType failed to run.

170209-17:24:36,47 workflow INFO:
     ***********************************
170209-17:24:36,47 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.extract_right_particles
170209-17:24:36,47 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172412-batmangh-extract_right_particles-7074cdad-687e-4beb-aab9-e0e6c1bcd1ef.pklz
170209-17:24:36,47 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.extract_left_particles
170209-17:24:36,47 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172436-batmangh-extract_left_particles-76dca266-4bb1-4d0a-ad58-1ebb86c0decb.pklz
170209-17:24:36,47 workflow INFO:
     ***********************************
Traceback (most recent call last):
  File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py", line 470, in <module>
    wf.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
    report_nodes_not_run(notrun)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[jcross186]

Hi Kayhan,

Double check that your build reflects the most recent version of the code. Your crash report indicates that ExtractParticlesFromChestRegionChestType is causing the problem. I fixed an error there, so it should be working.

I recommend getting things to work on the COPDGene case and then going from there. The default params might work fine for the low dose scan. If not, we can tune things to work for your data.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, February 9, 2017 at 5:35 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi James,

I pulled the develop version and rebuilt it. I still have the same issue. Not sure but it seems that in one of the steps it uses TEEM tools and it doesn't produce the results the rest of the pipeline expects; so it crashes. You can find the crash files here:

https://www.dropbox.com/s/xgbe7k8o1dzuofh/crash-20170209-165134-batmangh-fissure_particles_node-278f22bc-aaa5-4987-a2d0-8926143f0974.pklz?dl=0

I thought maybe my image is not good, so I applied on my of the COPDGene images. So it takes much longer. It produces different set of error, (see blow).

For my image, perhaps I should use different parameter since run time is very different? Is this pipeline appropriate for lowdose CT?

[batmangh@br006 CIP-build]$ python cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py --in_ct /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --out ~/test3.nrrd 170209-16:58:16,170 workflow INFO: ['check', 'execution', 'logging'] 170209-16:58:16,190 workflow INFO: Running serially. 170209-16:58:16,190 workflow INFO: Executing node generate_partial_lung_label_map in dir: /tmp/tmpTieWJa/LungLobeSegmentationWorkflow/generate_partial_lung_label_map 170209-16:58:16,194 workflow INFO: Running: GeneratePartialLungLabelMap --ict /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --olm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd 170209-16:58:22,632 interface INFO: stdout 2017-02-09T16:58:22.632485:Clipping low CT image values... 170209-16:58:23,134 interface INFO: stdout 2017-02-09T16:58:23.134029:Clipping upper CT image values... 170209-16:58:23,635 interface INFO: stdout 2017-02-09T16:58:23.635879:Executing partial lung filter... 170209-17:00:37,928 interface INFO: stdout 2017-02-09T17:00:37.927810:Writing lung mask image... 170209-17:00:43,535 interface INFO: stdout 2017-02-09T17:00:43.535154:DONE. 170209-17:00:44,51 workflow INFO: Executing node fissure_particles_node in dir: /tmp/tmpqN4ZT2/LungLobeSegmentationWorkflow/fissure_particles_node gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 17: Hessian eigenvector[1] gageQuerySet: expanded scalar query = ... 17: Hessian eigenvector[1] 15: Hessian eigenvectors 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 16: Hessian eigenvector[0] gageQuerySet: expanded scalar query = ... 16: Hessian eigenvector[0] 15: Hessian eigenvectors 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 1: value gageQuerySet: expanded scalar query = ... 1: value gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (1,0,0 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (1,0,0 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,0,0,0,0,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 18: Hessian eigenvector[2] gageQuerySet: expanded scalar query = ... 18: Hessian eigenvector[2] 15: Hessian eigenvectors 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 12: Hessian eigenvalue[0] gageQuerySet: expanded scalar query = ... 12: Hessian eigenvalue[0] 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 13: Hessian eigenvalue[1] gageQuerySet: expanded scalar query = ... 13: Hessian eigenvalue[1] 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 14: Hessian eigenvalue[2] gageQuerySet: expanded scalar query = ... 14: Hessian eigenvalue[2] 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 7: Hessian gageQuerySet: expanded scalar query = ... 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples gageKernelSet: which = 1 -> 00 gageKernelSet: which = 3 -> 11 gageKernelSet: which = 6 -> 22 gageQuerySet: original scalar query = ... 36: Hessian mode gageQuerySet: expanded scalar query = ... 36: Hessian mode 11: Hessian eigenvalues 7: Hessian gageUpdate: hello ____ context flags: 1=0 2=0 3=0 4=1 5=0 6=1 pvl flags: 1=1 2=1 3=0 _gagePvlNeedDUpdate: hello _gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1 _gagePvlNeedDUpdate: bye _gageNeedDUpdate: hello _gageNeedDUpdate: updating ctx's needD to (0,0,1 _gageNeedDUpdate: bye _gageNeedKUpdate: hello _gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0) _gageNeedKUpdate: bye _gageRadiusUpdate: hello _gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3 _gageRadiusUpdate: changing radius from 0 to 3 _gageRadiusUpdate: bye _gageCacheSizeUpdate: hello (radius = 3) _gageCacheSizeUpdate: bye _gageOffValueUpdate: hello _gageOffValueUpdate: bye gageUpdate: bye ^^^^^^^^^^^^^^^^^^^ gprobe: kernel support = 6^3 samples -o /tmp/tmpVyCQgR/cid_fissureParticles.vtk -b -i /tmp/tmpuXoDMo/pass3.nrrd -a NA -i /tmp/tmpuXoDMo/hevec1.nrrd -a hevec1 -i /tmp/tmpuXoDMo/hevec0.nrrd -a hevec0 -i /tmp/tmpuXoDMo/val.nrrd -a val -i /tmp/tmpuXoDMo/hevec2.nrrd -a hevec2 -i /tmp/tmpuXoDMo/heval0.nrrd -a h0 -i /tmp/tmpuXoDMo/heval1.nrrd -a h1 -i /tmp/tmpuXoDMo/heval2.nrrd -a h2 -i /tmp/tmpuXoDMo/hess.nrrd -a hess -i /tmp/tmpuXoDMo/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.742188,0.742188,0.5 --cipr UndefinedRegion --cipt Fissure Reading file for NA... Reading file for hevec1... Reading file for hevec0... Reading file for val... Reading file for hevec2... Reading file for h0... Reading file for h1... Reading file for h2... Reading file for hess... Reading file for hmode... Writing poly data... DONE. 170209-17:24:07,676 workflow INFO: Runtime memory and threads stats unavailable 170209-17:24:07,679 workflow INFO: Executing node pre_filter_fissure_particle_data in dir: /tmp/tmpNISiDz/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data 170209-17:24:07,683 workflow INFO: Running: FilterFissureParticleData --dist 3.000000 --ifp /tmp/tmpVyCQgR/cid_fissureParticles.vtk --ofp /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --size 110 170209-17:24:08,443 interface INFO: stdout 2017-02-09T17:24:08.443405:Reading polydata... 170209-17:24:08,443 interface INFO: stdout 2017-02-09T17:24:08.443405:Filtering particles using connectedness... 170209-17:24:09,455 interface INFO: stdout 2017-02-09T17:24:09.455189:Writing filtered particles ... 170209-17:24:09,455 interface INFO: stdout 2017-02-09T17:24:09.455189:DONE. 170209-17:24:09,969 workflow INFO: Executing node extract_right_particles in dir: /tmp/tmpZYYFz3/LungLobeSegmentationWorkflow/extract_right_particles 170209-17:24:09,974 workflow INFO: Running: ExtractParticlesFromChestRegionChestType --cipr RightLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_rightPreFilteredFissureParticles.vtk 170209-17:24:10,710 interface INFO: stdout 2017-02-09T17:24:10.710154:Reading polydata... 170209-17:24:10,710 interface INFO: stdout 2017-02-09T17:24:10.710154:Reading label map... 170209-17:24:12,737 workflow ERROR: ['Node extract_right_particles failed to run on host br006.pvt.bridges.psc.edu.'] 170209-17:24:12,739 workflow INFO: Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172412-batmangh-extract_right_particles-7074cdad-687e-4beb-aab9-e0e6c1bcd1ef.pklz 170209-17:24:12,739 workflow INFO: Traceback (most recent call last): File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run node.run(updatehash=updatehash) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run self._run_interface() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface self._result = self._run_command(execute) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command result = self._interface.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run runtime = self._run_wrapper(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper runtime = self._run_interface(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface self.raise_exception(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception raise RuntimeError(message) RuntimeError: Command: ExtractParticlesFromChestRegionChestType --cipr RightLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_rightPreFilteredFissureParticles.vtk Standard output: Reading polydata... Reading label map... Standard error:

Return code: -11 Interface ExtractParticlesFromChestRegionChestType failed to run.

170209-17:24:12,754 workflow INFO: Executing node generate_lobe_surface_models in dir: /tmp/tmpacLyHd/LungLobeSegmentationWorkflow/generate_lobe_surface_models 170209-17:24:12,759 workflow INFO: Running: GenerateLobeSurfaceModels --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpVyCQgR/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpVyCQgR/cid_rightLungLobesShapeModel.csv 170209-17:24:13,486 interface INFO: stdout 2017-02-09T17:24:13.486400:Read in 100 atlas resource file pairs. 170209-17:24:13,488 interface INFO: stdout 2017-02-09T17:24:13.486400:Reading fixed image... 170209-17:24:17,53 interface INFO: stdout 2017-02-09T17:24:17.052886:Subsampling fixed image... 170209-17:24:17,553 interface INFO: stdout 2017-02-09T17:24:17.553815:Reading moving image... 170209-17:24:18,565 interface INFO: stdout 2017-02-09T17:24:18.565348:Subsampling moving image... 170209-17:24:18,565 interface INFO: stdout 2017-02-09T17:24:18.565348:Extracting whole lung region from down sampled fixed image... 170209-17:24:18,565 interface INFO: stdout 2017-02-09T17:24:18.565348:Extracting whole lung region from down sampled moving image... 170209-17:24:18,565 interface INFO: stdout 2017-02-09T17:24:18.565348:Registering reference image to input image... 170209-17:24:27,747 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading transform from file... 170209-17:24:27,748 interface INFO: stdout 2017-02-09T17:24:27.747642:Reading fissure points from file... 170209-17:24:28,249 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,249 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,250 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading fissure points from file... 170209-17:24:28,251 interface INFO: stdout 2017-02-09T17:24:28.249522:Reading transform from file... 170209-17:24:28,251 interface INFO: stdout 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170209-17:24:28,753 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading fissure points from file... 170209-17:24:28,753 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading transform from file... 170209-17:24:28,753 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading fissure points from file... 170209-17:24:28,753 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading transform from file... 170209-17:24:28,754 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading fissure points from file... 170209-17:24:28,754 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading transform from file... 170209-17:24:28,754 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading fissure points from file... 170209-17:24:28,754 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading transform from file... 170209-17:24:28,754 interface INFO: stdout 2017-02-09T17:24:28.753375:Reading fissure points from file... 170209-17:24:28,754 interface INFO: stdout 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170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading fissure points from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading transform from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading fissure points from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading transform from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading fissure points from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading transform from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading fissure points from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading transform from file... 170209-17:24:29,257 interface INFO: stdout 2017-02-09T17:24:29.256075:Reading fissure points from file... 170209-17:24:29,257 interface INFO: stdout 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170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,766 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,767 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,767 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,767 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading transform from file... 170209-17:24:30,767 interface INFO: stdout 2017-02-09T17:24:30.765135:Reading fissure points from file... 170209-17:24:30,767 interface INFO: stdout 2017-02-09T17:24:30.765135:Getting range locations... 170209-17:24:32,799 interface INFO: stdout 2017-02-09T17:24:32.799802:Writing right shape model to file... 170209-17:24:32,800 interface INFO: stdout 2017-02-09T17:24:32.799802:Writing left shape model to file... 170209-17:24:32,800 interface INFO: stdout 2017-02-09T17:24:32.799802:DONE. 170209-17:24:33,317 workflow INFO: Executing node extract_left_particles in dir: /tmp/tmpt69OT0/LungLobeSegmentationWorkflow/extract_left_particles 170209-17:24:33,322 workflow INFO: Running: ExtractParticlesFromChestRegionChestType --cipr LeftLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_leftPreFilteredFissureParticles.vtk 170209-17:24:34,11 interface INFO: stdout 2017-02-09T17:24:34.011733:Reading polydata... 170209-17:24:34,12 interface INFO: stdout 2017-02-09T17:24:34.011733:Reading label map... 170209-17:24:36,36 workflow ERROR: ['Node extract_left_particles failed to run on host br006.pvt.bridges.psc.edu.'] 170209-17:24:36,37 workflow INFO: Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172436-batmangh-extract_left_particles-76dca266-4bb1-4d0a-ad58-1ebb86c0decb.pklz 170209-17:24:36,37 workflow INFO: Traceback (most recent call last): File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run node.run(updatehash=updatehash) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run self._run_interface() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface self._result = self._run_command(execute) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command result = self._interface.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run runtime = self._run_wrapper(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper runtime = self._run_interface(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface self.raise_exception(runtime) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception raise RuntimeError(message) RuntimeError: Command: ExtractParticlesFromChestRegionChestType --cipr LeftLung --ilm /tmp/tmpVyCQgR/cid_partialLungLabelMap.nrrd --ip /tmp/tmpVyCQgR/cid_preFilteredFissureParticles.vtk --op /tmp/tmpVyCQgR/cid_leftPreFilteredFissureParticles.vtk Standard output: Reading polydata... Reading label map... Standard error:

Return code: -11 Interface ExtractParticlesFromChestRegionChestType failed to run.

170209-17:24:36,47 workflow INFO:

---

170209-17:24:36,47 workflow ERROR: could not run node: LungLobeSegmentationWorkflow.extract_right_particles 170209-17:24:36,47 workflow INFO: crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172412-batmangh-extract_right_particles-7074cdad-687e-4beb-aab9-e0e6c1bcd1ef.pklz 170209-17:24:36,47 workflow ERROR: could not run node: LungLobeSegmentationWorkflow.extract_left_particles 170209-17:24:36,47 workflow INFO: crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-172436-batmangh-extract_left_particles-76dca266-4bb1-4d0a-ad58-1ebb86c0decb.pklz 170209-17:24:36,47 workflow INFO:

---

Traceback (most recent call last): File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py", line 470, in wf.run() File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run report_nodes_not_run(notrun) File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

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[kayhan-batmanghelich]

Hi James,

I am using the latest develop version (see below):

[batmangh@br005 ChestImagingPlatform-dev]$ git branch
  all
* develop
  master
[batmangh@br005 ChestImagingPlatform-dev]$ git pull
Already up-to-date.

am I missing something?

Good suggestion, I make sure it works on that COPGGene subject and we can go from there.

Thanks,

[kayhan-batmanghelich]

Hi Ross,

I just removed the build folder and rebuilt the CIP. I still get the same error. Are you sure, you pushed?

[batmangh@br005 CIP-build]$ python  cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py  --in_ct /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --out ~/test3.nrrd
170209-21:24:59,160 workflow INFO:
     ['check', 'execution', 'logging']
170209-21:24:59,198 workflow INFO:
     Running serially.
170209-21:24:59,198 workflow INFO:
     Executing node generate_partial_lung_label_map in dir: /tmp/tmpZRUzaZ/LungLobeSegmentationWorkflow/generate_partial_lung_label_map
170209-21:24:59,203 workflow INFO:
     Running:  GeneratePartialLungLabelMap  --ict /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --olm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd
170209-21:25:05,858 interface INFO:
     stdout 2017-02-09T21:25:05.858815:Clipping low CT image values...
170209-21:25:06,359 interface INFO:
     stdout 2017-02-09T21:25:06.359839:Clipping upper CT image values...
170209-21:25:06,861 interface INFO:
     stdout 2017-02-09T21:25:06.861316:Executing partial lung filter...
170209-21:27:21,160 interface INFO:
     stdout 2017-02-09T21:27:21.159828:Writing lung mask image...
170209-21:27:27,279 interface INFO:
     stdout 2017-02-09T21:27:27.278926:DONE.
170209-21:27:27,828 workflow INFO:
     Executing node generate_lobe_surface_models in dir: /tmp/tmpt3Rz0j/LungLobeSegmentationWorkflow/generate_lobe_surface_models
170209-21:27:27,834 workflow INFO:
     Running:  GenerateLobeSurfaceModels  --dir /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd --irlm /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpxzBQKo/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpxzBQKo/cid_rightLungLobesShapeModel.csv
170209-21:27:28,667 interface INFO:
     stdout 2017-02-09T21:27:28.666956:Read in 100 atlas resource file pairs.
170209-21:27:28,667 interface INFO:
     stdout 2017-02-09T21:27:28.666956:Reading fixed image...
170209-21:27:32,232 interface INFO:
     stdout 2017-02-09T21:27:32.232284:Subsampling fixed image...
170209-21:27:32,232 interface INFO:
     stdout 2017-02-09T21:27:32.232284:Reading moving image...
170209-21:27:33,754 interface INFO:
     stdout 2017-02-09T21:27:33.754614:Subsampling moving image...
170209-21:27:33,754 interface INFO:
     stdout 2017-02-09T21:27:33.754614:Extracting whole lung region from down sampled fixed image...
170209-21:27:33,755 interface INFO:
     stdout 2017-02-09T21:27:33.754614:Extracting whole lung region from down sampled moving image...
170209-21:27:33,755 interface INFO:
     stdout 2017-02-09T21:27:33.754614:Registering reference image to input image...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,448 interface INFO:
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170209-21:27:43,448 interface INFO:
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170209-21:27:43,448 interface INFO:
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170209-21:27:43,448 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,448 interface INFO:
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170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
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170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,449 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,450 interface INFO:
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170209-21:27:43,450 interface INFO:
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170209-21:27:43,450 interface INFO:
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170209-21:27:43,450 interface INFO:
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170209-21:27:43,450 interface INFO:
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170209-21:27:43,450 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,451 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,451 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,451 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,451 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,451 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading transform from file...
170209-21:27:43,451 interface INFO:
     stdout 2017-02-09T21:27:43.447810:Reading fissure points from file...
170209-21:27:43,451 interface INFO:
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170209-21:27:43,451 interface INFO:
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170209-21:27:43,451 interface INFO:
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170209-21:27:43,451 interface INFO:
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170209-21:27:43,451 interface INFO:
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     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,956 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,957 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,958 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading transform from file...
170209-21:27:43,959 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Reading fissure points from file...
170209-21:27:43,959 interface INFO:
     stdout 2017-02-09T21:27:43.955310:Getting range locations...
170209-21:27:45,991 interface INFO:
     stdout 2017-02-09T21:27:45.991725:Writing right shape model to file...
170209-21:27:45,991 interface INFO:
     stdout 2017-02-09T21:27:45.991725:Writing left shape model to file...
170209-21:27:45,992 interface INFO:
     stdout 2017-02-09T21:27:45.991725:DONE.
170209-21:27:46,506 workflow INFO:
     Executing node fissure_particles_node in dir: /tmp/tmpgVyYdZ/LungLobeSegmentationWorkflow/fissure_particles_node

gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     17: Hessian eigenvector[1]
gageQuerySet: expanded scalar query = ...
     17: Hessian eigenvector[1]
     15: Hessian eigenvectors
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     16: Hessian eigenvector[0]
gageQuerySet: expanded scalar query = ...
     16: Hessian eigenvector[0]
     15: Hessian eigenvectors
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
      1: value
gageQuerySet: expanded scalar query = ...
      1: value
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (1,0,0
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (1,0,0
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,0,0,0,0,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     18: Hessian eigenvector[2]
gageQuerySet: expanded scalar query = ...
     18: Hessian eigenvector[2]
     15: Hessian eigenvectors
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     12: Hessian eigenvalue[0]
gageQuerySet: expanded scalar query = ...
     12: Hessian eigenvalue[0]
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     13: Hessian eigenvalue[1]
gageQuerySet: expanded scalar query = ...
     13: Hessian eigenvalue[1]
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     14: Hessian eigenvalue[2]
gageQuerySet: expanded scalar query = ...
     14: Hessian eigenvalue[2]
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
      7: Hessian
gageQuerySet: expanded scalar query = ...
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
gageKernelSet: which = 1 -> 00
gageKernelSet: which = 3 -> 11
gageKernelSet: which = 6 -> 22
gageQuerySet: original scalar query = ...
     36: Hessian mode
gageQuerySet: expanded scalar query = ...
     36: Hessian mode
     11: Hessian eigenvalues
      7: Hessian
gageUpdate: hello ____________________
    context flags: 1=0 2=0 3=0 4=1 5=0 6=1
    pvl flags: 1=1 2=1 3=0
_gagePvlNeedDUpdate: hello
_gagePvlNeedDUpdate: updating pvl[0]'s needD to (0,0,1
_gagePvlNeedDUpdate: bye
_gageNeedDUpdate: hello
_gageNeedDUpdate: updating ctx's needD to (0,0,1
_gageNeedDUpdate: bye
_gageNeedKUpdate: hello
_gageNeedKUpdate: changing needK to (1,0,1,0,0,1,0)
_gageNeedKUpdate: bye
_gageRadiusUpdate: hello
_gageRadiusUpdate: k[00]=C4Hexic -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[11]=C4HexicD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: k[22]=C4HexicDD -> rad = 3 -> maxRad = 3
_gageRadiusUpdate: changing radius from 0 to 3
_gageRadiusUpdate: bye
_gageCacheSizeUpdate: hello (radius = 3)
_gageCacheSizeUpdate: bye
_gageOffValueUpdate: hello
_gageOffValueUpdate: bye
gageUpdate: bye ^^^^^^^^^^^^^^^^^^^
gprobe: kernel support = 6^3 samples
 -o /tmp/tmpxzBQKo/cid_fissureParticles.vtk -b -i /tmp/tmp36EAre/pass3.nrrd -a NA -i /tmp/tmp36EAre/hevec1.nrrd -a hevec1 -i /tmp/tmp36EAre/hevec0.nrrd -a hevec0 -i /tmp/tmp36EAre/val.nrrd -a val -i /tmp/tmp36EAre/hevec2.nrrd -a hevec2 -i /tmp/tmp36EAre/heval0.nrrd -a h0 -i /tmp/tmp36EAre/heval1.nrrd -a h1 -i /tmp/tmp36EAre/heval2.nrrd -a h2 -i /tmp/tmp36EAre/hess.nrrd -a hess -i /tmp/tmp36EAre/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.742188,0.742188,0.5 --cipr UndefinedRegion --cipt Fissure
Reading file for NA...
Reading file for hevec1...
Reading file for hevec0...
Reading file for val...
Reading file for hevec2...
Reading file for h0...
Reading file for h1...
Reading file for h2...
Reading file for hess...
Reading file for hmode...
Writing poly data...
DONE.
170209-21:52:33,174 workflow INFO:
     Runtime memory and threads stats unavailable
170209-21:52:33,178 workflow INFO:
     Executing node pre_filter_fissure_particle_data in dir: /tmp/tmpBK15C1/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data
170209-21:52:33,182 workflow INFO:
     Running:  FilterFissureParticleData  --dist 3.000000 --ifp /tmp/tmpxzBQKo/cid_fissureParticles.vtk --ofp /tmp/tmpxzBQKo/cid_preFilteredFissureParticles.vtk --size 110
170209-21:52:33,916 interface INFO:
     stdout 2017-02-09T21:52:33.916260:Reading polydata...
170209-21:52:33,917 interface INFO:
     stdout 2017-02-09T21:52:33.916260:Filtering particles using connectedness...
170209-21:52:34,928 interface INFO:
     stdout 2017-02-09T21:52:34.928454:Writing filtered particles ...
170209-21:52:35,429 interface INFO:
     stdout 2017-02-09T21:52:35.429416:DONE.
170209-21:52:35,944 workflow INFO:
     Executing node extract_right_particles in dir: /tmp/tmpCSFcL2/LungLobeSegmentationWorkflow/extract_right_particles
170209-21:52:35,949 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr RightLung --ilm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd --ip /tmp/tmpxzBQKo/cid_preFilteredFissureParticles.vtk --op /tmp/tmpxzBQKo/cid_rightPreFilteredFissureParticles.vtk
170209-21:52:36,647 interface INFO:
     stdout 2017-02-09T21:52:36.647683:Reading polydata...
170209-21:52:36,648 interface INFO:
     stdout 2017-02-09T21:52:36.647683:Reading label map...
170209-21:52:38,744 workflow ERROR:
     ['Node extract_right_particles failed to run on host br005.pvt.bridges.psc.edu.']
170209-21:52:38,818 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-215238-batmangh-extract_right_particles-0ac8d9a9-37ed-4eca-a021-74d358456fb4.pklz
170209-21:52:38,819 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
    self.raise_exception(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
 ExtractParticlesFromChestRegionChestType  --cipr RightLung --ilm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd --ip /tmp/tmpxzBQKo/cid_preFilteredFissureParticles.vtk --op /tmp/tmpxzBQKo/cid_rightPreFilteredFissureParticles.vtk
Standard output:
Reading polydata...
Reading label map...
Standard error:

Return code: -11
Interface ExtractParticlesFromChestRegionChestType failed to run.

170209-21:52:38,844 workflow INFO:
     Executing node extract_left_particles in dir: /tmp/tmpY4LOCF/LungLobeSegmentationWorkflow/extract_left_particles
170209-21:52:38,849 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr LeftLung --ilm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd --ip /tmp/tmpxzBQKo/cid_preFilteredFissureParticles.vtk --op /tmp/tmpxzBQKo/cid_leftPreFilteredFissureParticles.vtk
170209-21:52:39,470 interface INFO:
     stdout 2017-02-09T21:52:39.470369:Reading polydata...
170209-21:52:39,470 interface INFO:
     stdout 2017-02-09T21:52:39.470369:Reading label map...
170209-21:52:41,496 workflow ERROR:
     ['Node extract_left_particles failed to run on host br005.pvt.bridges.psc.edu.']
170209-21:52:41,496 workflow INFO:
     Saving crash info to /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-215241-batmangh-extract_left_particles-41c64c2d-0ba7-46b3-938c-55d2b1b251d6.pklz
170209-21:52:41,497 workflow INFO:
     Traceback (most recent call last):
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
    node.run(updatehash=updatehash)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
    self._run_interface()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
    self._result = self._run_command(execute)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
    result = self._interface.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
    self.raise_exception(runtime)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
 ExtractParticlesFromChestRegionChestType  --cipr LeftLung --ilm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd --ip /tmp/tmpxzBQKo/cid_preFilteredFissureParticles.vtk --op /tmp/tmpxzBQKo/cid_leftPreFilteredFissureParticles.vtk
Standard output:
Reading polydata...
Reading label map...
Standard error:

Return code: -11
Interface ExtractParticlesFromChestRegionChestType failed to run.

170209-21:52:41,507 workflow INFO:
     ***********************************
170209-21:52:41,507 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.extract_right_particles
170209-21:52:41,507 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-215238-batmangh-extract_right_particles-0ac8d9a9-37ed-4eca-a021-74d358456fb4.pklz
170209-21:52:41,507 workflow ERROR:
     could not run node: LungLobeSegmentationWorkflow.extract_left_particles
170209-21:52:41,508 workflow INFO:
     crashfile: /pylon1/ms4s88p/batmangh/gitSandbox/ChestImagingPlatform-dev/build/CIP-build/crash-20170209-215241-batmangh-extract_left_particles-41c64c2d-0ba7-46b3-938c-55d2b1b251d6.pklz
170209-21:52:41,508 workflow INFO:
     ***********************************
Traceback (most recent call last):
  File "cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py", line 470, in <module>
    wf.run()
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
    report_nodes_not_run(notrun)
  File "/home/batmangh/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[kayhan-batmanghelich]

I checked the line 8 of ExtractParticlesFromChestRegionChestType.cxx. This what I have:

#include "vtkDoubleArray.h"

That is the line you changed right. I think I have the latest version but there is still a bug.

Thanks,

[jcross186]

Hi Kayhan,

If you put the label map and the particles file on dropbox, I can take a look. Their location is indicated by the workflow output. E.g.:

ExtractParticlesFromChestRegionChestType --cipr RightLung --ilm /tmp/tmpxzBQKo/cid_partialLungLabelMap.nrrd --ip /tmp/tmpxzBQKo/cid_preFilteredFissureParticles.vtk --op /tmp/tmpxzBQKo/cid_rightPreFilteredFissureParticles.vtk

Let’s stick with the COPDGene case you’ve been working on, since I have access to it as well.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, February 9, 2017 at 10:04 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

I checked the line 8 of ExtractParticlesFromChestRegionChestType.cxx. This what I have:

include "vtkDoubleArray.h"

That is the line you changed right. I think I have the latest version but there is still a bug.

Thanks,

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/acil-bwh/ChestImagingPlatform/issues/14#issuecomment-278845561, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AD2glCjwR0FQ75POs5OkDKzEfH63_Phuks5ra9O2gaJpZM4L4khR.

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[kayhan-batmanghelich]

Hi James,

Sure that is a good idea. The intermediate files are here:

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0

generated with (id: 10004O):

python  cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py  --in_ct /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --out ~/test3.nrrd

Thanks

[jcross186]

Hi Kayhan,

My build works fine on that data.

I just committed a new version of ‘ExtractParticlesFromChestRegionChestType.cxx’ -- it just adds an additional print statement: “Extracting…”. Do an update in the develop branch and rebuild. Try executing just the ‘ExtractParticlesFromChestRegionChestType’ command printed out by the workfow. And let me know what you see. If you don’t see the “Extracting…” statement, then I would suggest doing a complete rebuild. Also, if you have other builds of the CIP, make sure there is not another one taking precedence in your path.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, February 10, 2017 at 10:36 AM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi James,

Sure that is a good idea. The intermediate files are here:

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0

generated with (id: 10004O):

python cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py --in_ct /pylon2/ms4s88p/jms565/projects/COPDGene/Images/10004O/10004O_INSP_STD_BWH_COPD.nhdr --out ~/test3.nrrd

Thanks

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[kayhan-batmanghelich]

I suggest adding install target to make, just to make sure the core functions are in one place.

[kayhan-batmanghelich]

Hi Ross,

You were right. The build was not clean. Now it is working for the COPDGene dataset and results looks good.

But on my data, it still produces an error. I guess the output of one of the steps is empty and this is why unu fails. I have uploaded the files here, you would give it a shot? I guess I have to change some param, do you have any suggestion?

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0 Thanks, Kayhan

[jcross186]

Hi Kayhan,

The format of the input CT should be nrrd. I just committed a small change to the workflow clarifying this in the help. You can use the ‘ReadWriteImageData’ command line tool to convert your data.

I ran the workflow on your (converted) data, and the output looks pretty good. The right lung segmentation fits the fissure boundaries ok, but you might want to play with the —reg parameter, which controls shape regularization during the lobe boundary shape fitting stage. You might be able to get a better fit by letting the fit be more flexible.

Give that a shot and let me know if you still have questions.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Saturday, February 11, 2017 at 1:09 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi Ross,

You were right. The build was not clean. Now it is working for the COPDGene dataset and results looks good.

But on my data, it still produces an error. I guess the output of one of the steps is empty and this is why unu fails. I have uploaded the files here, you would give it a shot? I guess I have to change some param, do you have any suggestion?

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0 Thanks, Kayhan

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/acil-bwh/ChestImagingPlatform/issues/14#issuecomment-279164503, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AD2glNymXZLfR-JD6Q2s5B1KqaGPRWNBks5rbfl2gaJpZM4L4khR.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

[kayhan-batmanghelich]

Thanks, James. I will give it a shot. Do you have any good reference (papers) about the pipeline?

Kayhan

On Sat, Feb 11, 2017 at 2:25 PM, jcross186 notifications@github.com wrote:

Hi Kayhan,

The format of the input CT should be nrrd. I just committed a small change to the workflow clarifying this in the help. You can use the ‘ReadWriteImageData’ command line tool to convert your data.

I ran the workflow on your (converted) data, and the output looks pretty good. The right lung segmentation fits the fissure boundaries ok, but you might want to play with the —reg parameter, which controls shape regularization during the lobe boundary shape fitting stage. You might be able to get a better fit by letting the fit be more flexible.

Give that a shot and let me know if you still have questions.

-James

From: Kayhan Batmanghelich <notifications@github.com<mailto: notifications@github.com>> Reply-To: acil-bwh/ChestImagingPlatform <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Saturday, February 11, 2017 at 1:09 PM To: acil-bwh/ChestImagingPlatform <ChestImagingPlatform@noreply.github.com mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi Ross,

You were right. The build was not clean. Now it is working for the COPDGene dataset and results looks good.

But on my data, it still produces an error. I guess the output of one of the steps is empty and this is why unu fails. I have uploaded the files here, you would give it a shot? I guess I have to change some param, do you have any suggestion?

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0 Thanks, Kayhan

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ acil-bwh/ChestImagingPlatform/issues/14#issuecomment-279164503, or mute the threadhttps://github.com/notifications/unsubscribe- auth/AD2glNymXZLfR-JD6Q2s5B1KqaGPRWNBks5rbfl2gaJpZM4L4khR.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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[jcross186]

The best reference is: http://robobees.seas.harvard.edu/files/acil/files/med_phys_2013_ross.pdf

There have been a few modifications to the algorithm since the paper, namely the shape regularization term and the ability to add particles data sets for other structures (vessels and airways) to guide the shape fitting process. Also, the final thin plate spline that determines the boundaries between the lobes is now a blend of the TPS from the shape fitting and the TPS that goes through the fissure particles: in areas where there are no fissure particles, the shape-fit boundary gets more weight. Overall, though, the referenced paper describes the main stages in the algorithm.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Saturday, February 11, 2017 at 3:12 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Thanks, James. I will give it a shot. Do you have any good reference (papers) about the pipeline?

Kayhan

On Sat, Feb 11, 2017 at 2:25 PM, jcross186 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Kayhan,

The format of the input CT should be nrrd. I just committed a small change to the workflow clarifying this in the help. You can use the ‘ReadWriteImageData’ command line tool to convert your data.

I ran the workflow on your (converted) data, and the output looks pretty good. The right lung segmentation fits the fissure boundaries ok, but you might want to play with the —reg parameter, which controls shape regularization during the lobe boundary shape fitting stage. You might be able to get a better fit by letting the fit be more flexible.

Give that a shot and let me know if you still have questions.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com<mailto: reply@reply.github.commailto:reply@reply.github.com>> Date: Saturday, February 11, 2017 at 1:09 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edumailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.commailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi Ross,

You were right. The build was not clean. Now it is working for the COPDGene dataset and results looks good.

But on my data, it still produces an error. I guess the output of one of the steps is empty and this is why unu fails. I have uploaded the files here, you would give it a shot? I guess I have to change some param, do you have any suggestion?

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0 Thanks, Kayhan

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ acil-bwh/ChestImagingPlatform/issues/14#issuecomment-279164503, or mute the threadhttps://github.com/notifications/unsubscribe- auth/AD2glNymXZLfR-JD6Q2s5B1KqaGPRWNBks5rbfl2gaJpZM4L4khR.

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[kayhan-batmanghelich]

Thank you, it is an amazing code. Thank you for sharing it.

On Sat, Feb 11, 2017 at 4:02 PM, jcross186 notifications@github.com wrote:

The best reference is: http://robobees.seas.harvard. edu/files/acil/files/med_phys_2013_ross.pdf

There have been a few modifications to the algorithm since the paper, namely the shape regularization term and the ability to add particles data sets for other structures (vessels and airways) to guide the shape fitting process. Also, the final thin plate spline that determines the boundaries between the lobes is now a blend of the TPS from the shape fitting and the TPS that goes through the fissure particles: in areas where there are no fissure particles, the shape-fit boundary gets more weight. Overall, though, the referenced paper describes the main stages in the algorithm.

-James

From: Kayhan Batmanghelich <notifications@github.com<mailto: notifications@github.com>> Reply-To: acil-bwh/ChestImagingPlatform <reply@reply.github.com<mailto: reply@reply.github.com>> Date: Saturday, February 11, 2017 at 3:12 PM To: acil-bwh/ChestImagingPlatform <ChestImagingPlatform@noreply.github.com mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Thanks, James. I will give it a shot. Do you have any good reference (papers) about the pipeline?

Kayhan

On Sat, Feb 11, 2017 at 2:25 PM, jcross186 <notifications@github.com< mailto:notifications@github.com>> wrote:

Hi Kayhan,

The format of the input CT should be nrrd. I just committed a small change to the workflow clarifying this in the help. You can use the ‘ReadWriteImageData’ command line tool to convert your data.

I ran the workflow on your (converted) data, and the output looks pretty good. The right lung segmentation fits the fissure boundaries ok, but you might want to play with the —reg parameter, which controls shape regularization during the lobe boundary shape fitting stage. You might be able to get a better fit by letting the fit be more flexible.

Give that a shot and let me know if you still have questions.

-James

From: Kayhan Batmanghelich <notifications@github.com<mailto: notifications@github.com><mailto: notifications@github.commailto:notifications@github.com>> Reply-To: acil-bwh/ChestImagingPlatform <reply@reply.github.com<mailto: reply@reply.github.com><mailto: reply@reply.github.commailto:reply@reply.github.com>> Date: Saturday, February 11, 2017 at 1:09 PM To: acil-bwh/ChestImagingPlatform <ChestImagingPlatform@noreply. github.commailto:ChestImagingPlatform@noreply.github.com mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross <jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu mailto:jross@bwh.harvard.edu>, Comment <comment@noreply.github.com<mailto:comment@noreply.github.com mailto:comment@noreply.github.com>

Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi Ross,

You were right. The build was not clean. Now it is working for the COPDGene dataset and results looks good.

But on my data, it still produces an error. I guess the output of one of the steps is empty and this is why unu fails. I have uploaded the files here, you would give it a shot? I guess I have to change some param, do you have any suggestion?

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp- wDU1IMfsiY4XKyDgXKa?dl=0 Thanks, Kayhan

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ acil-bwh/ChestImagingPlatform/issues/14#issuecomment-279164503, or mute the threadhttps://github.com/notifications/unsubscribe- auth/AD2glNymXZLfR-JD6Q2s5B1KqaGPRWNBks5rbfl2gaJpZM4L4khR.

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[kayhan-batmanghelich]

Hi James,

I was wondering when you run the code on my data, did it finish ? It has been running for 5 hours and it is not finished yet. Using top, it show it is running FitLobeSurfaceModel. On the COPDGene data, it finished in less than an hour. This is the output so far:

/home/batmangh/MyPylon2Space/Projects/shirALI/scripts/segmentLobes.py --in_ct /home/batmangh/MyPylon2Space/LUNA16/subset0/1.3.6.1.4.1.14519.5.2.1.6279.6001.108197895896446896160048741492.mhd --out_ct /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --out_lbl /home/batmangh/MyPylon2Space/LUNA16/subset0/lbl.nrrd --out_lob /home/batmangh/MyPylon2Space/LUNA16/subset0/lob.nrrd --out_iso_ct /home/batmangh/MyPylon2Space/LUNA16/subset0/img_iso.nrrd --out_iso_lbl /home/batmangh/MyPylon2Space/LUNA16/subset0/lbl_iso.nrrd --out_iso_lob /home/batmangh/MyPylon2Space/LUNA16/subset0/lob_iso.nrrd
$ /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/bin/ReadWriteImageData --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/1.3.6.1.4.1.14519.5.2.1.6279.6001.108197895896446896160048741492.mhd --oct /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd (simulated)
$ /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/bin/GeneratePartialLungLabelMap --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --olm /home/batmangh/MyPylon2Space/LUNA16/subset0/lbl.nrrd (simulated)
170213-19:01:09,340 workflow INFO:
     ['check', 'execution', 'logging']
170213-19:01:10,430 workflow INFO:
     Running serially.
170213-19:01:10,432 workflow INFO:
     Executing node generate_partial_lung_label_map in dir: /tmp/tmpLpSTX2/LungLobeSegmentationWorkflow/generate_partial_lung_label_map
170213-19:01:10,443 workflow INFO:
     Running:  GeneratePartialLungLabelMap  --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --olm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd
170213-19:01:13,207 interface INFO:
     stdout 2017-02-13T19:01:13.207733:Clipping low CT image values...
170213-19:01:13,208 interface INFO:
     stdout 2017-02-13T19:01:13.207733:Clipping upper CT image values...
170213-19:01:13,208 interface INFO:
     stdout 2017-02-13T19:01:13.207733:Executing partial lung filter...
170213-19:01:40,782 interface INFO:
     stdout 2017-02-13T19:01:40.782446:Writing lung mask image...
170213-19:01:41,794 interface INFO:
     stdout 2017-02-13T19:01:41.794386:DONE.
170213-19:01:42,338 workflow INFO:
     Executing node generate_lobe_surface_models in dir: /tmp/tmpFZsk4X/LungLobeSegmentationWorkflow/generate_lobe_surface_models
170213-19:01:42,355 workflow INFO:
     Running:  GenerateLobeSurfaceModels  --dir /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd --irlm /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpBAykls/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpBAykls/cid_rightLungLobesShapeModel.csv
170213-19:01:43,195 interface INFO:
     stdout 2017-02-13T19:01:43.195598:Read in 100 atlas resource file pairs.
170213-19:01:43,196 interface INFO:
     stdout 2017-02-13T19:01:43.195598:Reading fixed image...
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     stdout 2017-02-13T19:01:43.697033:Subsampling fixed image...
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     stdout 2017-02-13T19:01:43.697033:Reading moving image...
170213-19:01:45,219 interface INFO:
     stdout 2017-02-13T19:01:45.219116:Subsampling moving image...
170213-19:01:45,219 interface INFO:
     stdout 2017-02-13T19:01:45.219116:Extracting whole lung region from down sampled fixed image...
170213-19:01:45,219 interface INFO:
     stdout 2017-02-13T19:01:45.219116:Extracting whole lung region from down sampled moving image...
170213-19:01:45,219 interface INFO:
     stdout 2017-02-13T19:01:45.219116:Registering reference image to input image...
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     stdout 2017-02-13T19:01:46.741734:Reading transform from file...
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     stdout 2017-02-13T19:01:51.266988:Reading transform from file...
170213-19:01:51,268 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading fissure points from file...
170213-19:01:51,268 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading transform from file...
170213-19:01:51,268 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading fissure points from file...
170213-19:01:51,268 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading transform from file...
170213-19:01:51,269 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading fissure points from file...
170213-19:01:51,269 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading transform from file...
170213-19:01:51,269 interface INFO:
     stdout 2017-02-13T19:01:51.266988:Reading fissure points from file...
170213-19:01:51,770 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,770 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,770 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,770 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,770 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,771 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,772 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:51,772 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading fissure points from file...
170213-19:01:51,772 interface INFO:
     stdout 2017-02-13T19:01:51.769934:Reading transform from file...
170213-19:01:52,273 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,273 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,273 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,277 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,277 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,278 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading transform from file...
170213-19:01:52,279 interface INFO:
     stdout 2017-02-13T19:01:52.272995:Reading fissure points from file...
170213-19:01:52,780 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading transform from file...
170213-19:01:52,780 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading fissure points from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading transform from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading fissure points from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading transform from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading fissure points from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading transform from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading fissure points from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading transform from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading fissure points from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading transform from file...
170213-19:01:52,781 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Reading fissure points from file...
170213-19:01:52,782 interface INFO:
     stdout 2017-02-13T19:01:52.780588:Getting range locations...
170213-19:01:55,325 interface INFO:
     stdout 2017-02-13T19:01:55.325200:Writing right shape model to file...
170213-19:01:55,325 interface INFO:
     stdout 2017-02-13T19:01:55.325200:Writing left shape model to file...
170213-19:01:55,325 interface INFO:
     stdout 2017-02-13T19:01:55.325200:DONE.
170213-19:01:55,861 workflow INFO:
     Executing node fissure_particles_node in dir: /tmp/tmp6Qol8C/LungLobeSegmentationWorkflow/fissure_particles_node
Reading file for NA...
Reading file for hevec1...
Reading file for hevec0...
Reading file for val...
Reading file for hevec2...
Reading file for h0...
Reading file for h1...
Reading file for h2...
Reading file for hess...
Reading file for hmode...
Writing poly data...
DONE.
 -o /tmp/tmpBAykls/cid_fissureParticles.vtk -b -i /tmp/tmpuaG81Y/pass3.nrrd -a NA -i /tmp/tmpuaG81Y/hevec1.nrrd -a hevec1 -i /tmp/tmpuaG81Y/hevec0.nrrd -a hevec0 -i /tmp/tmpuaG81Y/val.nrrd -a val -i /tmp/tmpuaG81Y/hevec2.nrrd -a hevec2 -i /tmp/tmpuaG81Y/heval0.nrrd -a h0 -i /tmp/tmpuaG81Y/heval1.nrrd -a h1 -i /tmp/tmpuaG81Y/heval2.nrrd -a h2 -i /tmp/tmpuaG81Y/hess.nrrd -a hess -i /tmp/tmpuaG81Y/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.859375,0.859375,2.5 --cipr UndefinedRegion --cipt Fissure
170213-20:10:03,787 workflow INFO:
     Runtime memory and threads stats unavailable
170213-20:10:03,793 workflow INFO:
     Executing node pre_filter_fissure_particle_data in dir: /tmp/tmpQ6pIIW/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data
170213-20:10:03,798 workflow INFO:
     Running:  FilterFissureParticleData  --dist 3.000000 --ifp /tmp/tmpBAykls/cid_fissureParticles.vtk --ofp /tmp/tmpBAykls/cid_preFilteredFissureParticles.vtk --size 110
170213-20:10:04,565 interface INFO:
     stdout 2017-02-13T20:10:04.565028:Reading polydata...
170213-20:10:04,566 interface INFO:
     stdout 2017-02-13T20:10:04.565028:Filtering particles using connectedness...
170213-20:10:08,642 interface INFO:
     stdout 2017-02-13T20:10:08.642286:Writing filtered particles ...
170213-20:10:08,642 interface INFO:
     stdout 2017-02-13T20:10:08.642286:DONE.
170213-20:10:09,179 workflow INFO:
     Executing node extract_left_particles in dir: /tmp/tmpNuvKxX/LungLobeSegmentationWorkflow/extract_left_particles
170213-20:10:09,188 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr LeftLung --ilm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd --ip /tmp/tmpBAykls/cid_preFilteredFissureParticles.vtk --op /tmp/tmpBAykls/cid_leftPreFilteredFissureParticles.vtk
170213-20:10:09,965 interface INFO:
     stdout 2017-02-13T20:10:09.964944:Reading polydata...
170213-20:10:09,965 interface INFO:
     stdout 2017-02-13T20:10:09.964944:Extracting...
170213-20:10:09,965 interface INFO:
     stdout 2017-02-13T20:10:09.964944:Reading label map...
170213-20:10:10,475 interface INFO:
     stdout 2017-02-13T20:10:10.474931:Writing extracted particles...
170213-20:10:11,487 interface INFO:
     stdout 2017-02-13T20:10:11.487267:DONE.
170213-20:10:12,22 workflow INFO:
     Executing node extract_right_particles in dir: /tmp/tmpvtivDN/LungLobeSegmentationWorkflow/extract_right_particles
170213-20:10:12,29 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr RightLung --ilm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd --ip /tmp/tmpBAykls/cid_preFilteredFissureParticles.vtk --op /tmp/tmpBAykls/cid_rightPreFilteredFissureParticles.vtk
170213-20:10:12,755 interface INFO:
     stdout 2017-02-13T20:10:12.754932:Reading polydata...
170213-20:10:12,755 interface INFO:
     stdout 2017-02-13T20:10:12.754932:Extracting...
170213-20:10:12,755 interface INFO:
     stdout 2017-02-13T20:10:12.754932:Reading label map...
170213-20:10:13,767 interface INFO:
     stdout 2017-02-13T20:10:13.767433:Writing extracted particles...
170213-20:10:14,779 interface INFO:
     stdout 2017-02-13T20:10:14.779378:DONE.
170213-20:10:15,331 workflow INFO:
     Executing node fit_lobe_surface_models_to_particle_data in dir: /tmp/tmpNlAabr/LungLobeSegmentationWorkflow/fit_lobe_surface_models_to_particle_data
170213-20:10:15,339 workflow INFO:
     Running:  FitLobeSurfaceModelsToParticleData  --ilfp /tmp/tmpBAykls/cid_leftPreFilteredFissureParticles.vtk --ilsm /tmp/tmpBAykls/cid_leftLungLobesShapeModel.csv --irfp /tmp/tmpBAykls/cid_rightPreFilteredFissureParticles.vtk --irsm /tmp/tmpBAykls/cid_rightLungLobesShapeModel.csv --iters 200 --olsm /tmp/tmpBAykls/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpBAykls/cid_rightLungLobesShapeModel.csv --reg 50.000000
170213-20:10:16,113 interface INFO:
     stdout 2017-02-13T20:10:16.112776:Reading left lung fissure particles...
170213-20:10:16,614 interface INFO:
     stdout 2017-02-13T20:10:16.614101:Asserting chest-region chest-type existence...
170213-20:10:16,614 interface INFO:
     stdout 2017-02-13T20:10:16.614101:Reading right lung fissure particles...
170213-20:10:17,625 interface INFO:
     stdout 2017-02-13T20:10:17.625677:Asserting chest-region chest-type existence...
170213-20:10:17,626 interface INFO:
     stdout 2017-02-13T20:10:17.625677:Reading left surface model...
170213-20:10:17,626 interface INFO:
     stdout 2017-02-13T20:10:17.625677:Fraction variance explained by modes used in left surface model: 0.992118
170213-20:10:17,626 interface INFO:
     stdout 2017-02-13T20:10:17.625677:Reading right surface model...
170213-20:10:17,626 interface INFO:
     stdout 2017-02-13T20:10:17.625677:Fraction variance explained by modes used in right surface model:    0.977813
170213-20:10:17,626 interface INFO:
     stdout 2017-02-13T20:10:17.625677:Executing Nelder-Mead optimizer (left lung)...
170213-20:11:25,538 interface INFO:
     stdout 2017-02-13T20:11:25.538208:val: -8836.71
170213-20:11:40,341 interface INFO:
     stdout 2017-02-13T20:11:40.341000:val: -10410.2
170213-20:11:46,458 interface INFO:
     stdout 2017-02-13T20:11:46.458330:val: -10410.2
170213-20:11:53,86 interface INFO:
     stdout 2017-02-13T20:11:53.086415:val: -10410.2
170213-20:12:07,887 interface INFO:
     stdout 2017-02-13T20:12:07.886989:val: -10482.6
170213-20:12:19,111 interface INFO:
     stdout 2017-02-13T20:12:19.111235:val: -10609.2
170213-20:12:26,250 interface INFO:
     stdout 2017-02-13T20:12:26.250156:val: -10609.2
170213-20:12:33,388 interface INFO:
     stdout 2017-02-13T20:12:33.388359:val: -10609.2
170213-20:12:46,656 interface INFO:
     stdout 2017-02-13T20:12:46.656392:val: -10609.2
170213-20:12:53,284 interface INFO:
     stdout 2017-02-13T20:12:53.284871:val: -10609.2
170213-20:13:06,551 interface INFO:
     stdout 2017-02-13T20:13:06.551632:val: -10609.2
170213-20:13:20,840 interface INFO:
     stdout 2017-02-13T20:13:20.840211:val: -10812.3
170213-20:13:37,683 interface INFO:
     stdout 2017-02-13T20:13:37.682908:val: -10812.3
170213-20:13:55,547 interface INFO:
     stdout 2017-02-13T20:13:55.547448:val: -10927.1
170213-20:14:04,220 interface INFO:
     stdout 2017-02-13T20:14:04.220723:val: -10927.1
170213-20:14:22,85 interface INFO:
     stdout 2017-02-13T20:14:22.085410:val: -10927.1
170213-20:14:29,226 interface INFO:
     stdout 2017-02-13T20:14:29.225944:val: -10927.1
170213-20:14:49,646 interface INFO:
     stdout 2017-02-13T20:14:49.646179:val: -11081.3
170213-20:14:59,340 interface INFO:
     stdout 2017-02-13T20:14:59.340565:val: -11081.3
170213-20:15:07,503 interface INFO:
     stdout 2017-02-13T20:15:07.503030:val: -11081.3
170213-20:15:24,857 interface INFO:
     stdout 2017-02-13T20:15:24.857508:val: -11159.6
170213-20:15:34,40 interface INFO:
     stdout 2017-02-13T20:15:34.040452:val: -11159.6
170213-20:15:50,885 interface INFO:
     stdout 2017-02-13T20:15:50.885259:val: -11159.6
170213-20:16:00,579 interface INFO:
     stdout 2017-02-13T20:16:00.579303:val: -11159.6
170213-20:16:07,719 interface INFO:
     stdout 2017-02-13T20:16:07.719192:val: -11159.6
170213-20:16:23,543 interface INFO:
     stdout 2017-02-13T20:16:23.542844:val: -11303.4
170213-20:16:40,388 interface INFO:
     stdout 2017-02-13T20:16:40.387918:val: -11303.4
170213-20:17:00,299 interface INFO:
     stdout 2017-02-13T20:17:00.299013:val: -11303.4
170213-20:17:16,633 interface INFO:
     stdout 2017-02-13T20:17:16.632838:val: -11303.4
170213-20:17:26,330 interface INFO:
     stdout 2017-02-13T20:17:26.330368:val: -11303.4
170213-20:17:43,175 interface INFO:
     stdout 2017-02-13T20:17:43.174901:val: -11303.4
170213-20:17:51,847 interface INFO:
     stdout 2017-02-13T20:17:51.847569:val: -11303.4
170213-20:18:08,185 interface INFO:
     stdout 2017-02-13T20:18:08.185015:val: -11303.4
170213-20:18:24,6 interface INFO:
     stdout 2017-02-13T20:18:24.006709:val: -11400.4
170213-20:18:31,657 interface INFO:
     stdout 2017-02-13T20:18:31.657717:val: -11400.4
170213-20:18:44,926 interface INFO:
     stdout 2017-02-13T20:18:44.925924:val: -11400.4
170213-20:18:52,577 interface INFO:
     stdout 2017-02-13T20:18:52.576903:val: -11400.4
170213-20:19:00,227 interface INFO:
     stdout 2017-02-13T20:19:00.227248:val: -11400.4
170213-20:19:17,74 interface INFO:
     stdout 2017-02-13T20:19:17.074344:val: -11400.4
170213-20:19:32,897 interface INFO:
     stdout 2017-02-13T20:19:32.897351:val: -11400.4
170213-20:19:39,528 interface INFO:
     stdout 2017-02-13T20:19:39.528565:val: -11400.4
170213-20:19:57,906 interface INFO:
     stdout 2017-02-13T20:19:57.906474:val: -11471.7
170213-20:20:06,578 interface INFO:
     stdout 2017-02-13T20:20:06.578203:val: -11471.7
170213-20:20:21,892 interface INFO:
     stdout 2017-02-13T20:20:21.891664:val: -11471.7
170213-20:20:36,183 interface INFO:
     stdout 2017-02-13T20:20:36.182505:val: -11471.7
170213-20:20:44,347 interface INFO:
     stdout 2017-02-13T20:20:44.347306:val: -11471.7
170213-20:20:53,20 interface INFO:
     stdout 2017-02-13T20:20:53.020732:val: -11471.7
170213-20:21:09,353 interface INFO:
     stdout 2017-02-13T20:21:09.353059:val: -11488.2
170213-20:21:17,518 interface INFO:
     stdout 2017-02-13T20:21:17.518187:val: -11488.2
170213-20:21:33,852 interface INFO:
     stdout 2017-02-13T20:21:33.852167:val: -11489.7
170213-20:21:43,36 interface INFO:
     stdout 2017-02-13T20:21:43.035824:val: -11489.7
170213-20:21:52,219 interface INFO:
     stdout 2017-02-13T20:21:52.219247:val: -11489.7
170213-20:22:05,999 interface INFO:
     stdout 2017-02-13T20:22:05.999708:val: -11565.1
170213-20:22:18,244 interface INFO:
     stdout 2017-02-13T20:22:18.244523:val: -11565.1
170213-20:22:24,361 interface INFO:
     stdout 2017-02-13T20:22:24.361920:val: -11565.1
170213-20:22:36,608 interface INFO:
     stdout 2017-02-13T20:22:36.608228:val: -11565.1
170213-20:22:49,363 interface INFO:
     stdout 2017-02-13T20:22:49.363416:val: -11565.1
170213-20:23:02,119 interface INFO:
     stdout 2017-02-13T20:23:02.118914:val: -11565.1
170213-20:23:08,238 interface INFO:
     stdout 2017-02-13T20:23:08.238598:val: -11565.1
170213-20:23:20,484 interface INFO:
     stdout 2017-02-13T20:23:20.484082:val: -11565.1
170213-20:23:26,601 interface INFO:
     stdout 2017-02-13T20:23:26.601205:val: -11565.1
170213-20:23:32,718 interface INFO:
     stdout 2017-02-13T20:23:32.718164:val: -11565.1
170213-20:23:38,836 interface INFO:
     stdout 2017-02-13T20:23:38.835957:val: -11565.1
170213-20:23:51,592 interface INFO:
     stdout 2017-02-13T20:23:51.592172:val: -11565.1
170213-20:24:03,839 interface INFO:
     stdout 2017-02-13T20:24:03.839230:val: -11565.1
170213-20:24:09,957 interface INFO:
     stdout 2017-02-13T20:24:09.957102:val: -11565.1
170213-20:24:22,201 interface INFO:
     stdout 2017-02-13T20:24:22.201526:val: -11565.1
170213-20:24:28,319 interface INFO:
     stdout 2017-02-13T20:24:28.319361:val: -11565.1
170213-20:24:34,947 interface INFO:
     stdout 2017-02-13T20:24:34.947263:val: -11565.1
170213-20:24:41,64 interface INFO:
     stdout 2017-02-13T20:24:41.064258:val: -11565.1
170213-20:24:47,184 interface INFO:
     stdout 2017-02-13T20:24:47.183978:val: -11565.1
170213-20:24:59,429 interface INFO:
     stdout 2017-02-13T20:24:59.429256:val: -11565.1
170213-20:25:12,185 interface INFO:
     stdout 2017-02-13T20:25:12.184900:val: -11575.7
170213-20:25:24,431 interface INFO:
     stdout 2017-02-13T20:25:24.431350:val: -11575.7
170213-20:25:37,187 interface INFO:
     stdout 2017-02-13T20:25:37.187315:val: -11584
170213-20:25:43,815 interface INFO:
     stdout 2017-02-13T20:25:43.815272:val: -11584
170213-20:25:49,933 interface INFO:
     stdout 2017-02-13T20:25:49.933262:val: -11584
170213-20:25:56,563 interface INFO:
     stdout 2017-02-13T20:25:56.563837:val: -11584
170213-20:26:09,319 interface INFO:
     stdout 2017-02-13T20:26:09.318968:val: -11609.6
170213-20:26:15,436 interface INFO:
     stdout 2017-02-13T20:26:15.436383:val: -11609.6
170213-20:26:28,192 interface INFO:
     stdout 2017-02-13T20:26:28.192471:val: -11609.6
170213-20:26:34,310 interface INFO:
     stdout 2017-02-13T20:26:34.310211:val: -11609.6
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     stdout 2017-02-13T20:26:40.938306:val: -11609.6
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     stdout 2017-02-13T20:26:47.055265:val: -11609.6
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     stdout 2017-02-13T20:26:53.683639:val: -11609.6
170213-20:27:00,312 interface INFO:
     stdout 2017-02-13T20:27:00.312160:val: -11609.6
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     stdout 2017-02-13T20:27:06.429048:val: -11609.6
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     stdout 2017-02-13T20:27:13.057681:val: -11609.6
170213-20:27:26,323 interface INFO:
     stdout 2017-02-13T20:27:26.323547:val: -11609.6
170213-20:27:39,588 interface INFO:
     stdout 2017-02-13T20:27:39.588630:val: -11618.5
170213-20:27:46,216 interface INFO:
     stdout 2017-02-13T20:27:46.216632:val: -11618.5
170213-20:27:52,845 interface INFO:
     stdout 2017-02-13T20:27:52.845631:val: -11618.5
170213-20:27:59,474 interface INFO:
     stdout 2017-02-13T20:27:59.473946:val: -11618.5
170213-20:28:06,101 interface INFO:
     stdout 2017-02-13T20:28:06.101633:val: -11618.5
170213-20:28:12,729 interface INFO:
     stdout 2017-02-13T20:28:12.729186:val: -11618.5
170213-20:28:25,995 interface INFO:
     stdout 2017-02-13T20:28:25.995311:val: -11618.5
170213-20:28:39,265 interface INFO:
     stdout 2017-02-13T20:28:39.264957:val: -11618.5
170213-20:28:53,42 interface INFO:
     stdout 2017-02-13T20:28:53.042293:val: -11620.7
170213-20:28:59,670 interface INFO:
     stdout 2017-02-13T20:28:59.670183:val: -11620.7
170213-20:29:13,448 interface INFO:
     stdout 2017-02-13T20:29:13.448527:val: -11620.7
170213-20:29:20,76 interface INFO:
     stdout 2017-02-13T20:29:20.076770:val: -11620.7
170213-20:29:26,704 interface INFO:
     stdout 2017-02-13T20:29:26.704928:val: -11620.7
170213-20:29:39,970 interface INFO:
     stdout 2017-02-13T20:29:39.970718:val: -11621.3
170213-20:29:53,236 interface INFO:
     stdout 2017-02-13T20:29:53.236615:val: -11621.7
170213-20:30:07,14 interface INFO:
     stdout 2017-02-13T20:30:07.014435:val: -11621.7
170213-20:30:20,789 interface INFO:
     stdout 2017-02-13T20:30:20.789879:val: -11622.7
170213-20:30:33,545 interface INFO:
     stdout 2017-02-13T20:30:33.545636:val: -11622.7
170213-20:30:47,323 interface INFO:
     stdout 2017-02-13T20:30:47.323615:val: -11625.7
170213-20:31:00,589 interface INFO:
     stdout 2017-02-13T20:31:00.589628:val: -11627.5
170213-20:31:07,217 interface INFO:
     stdout 2017-02-13T20:31:07.217337:val: -11627.5
170213-20:31:20,995 interface INFO:
     stdout 2017-02-13T20:31:20.995598:val: -11627.5

Thanks,

[jcross186]

Hi Kayhan,

The algorithm completed within a reasonable time on my machine for your data. You might simply try rerunning. It could be that there is something going on with the shape fitting optimizer. Does each iteration take a very long time, or does the algorithm just hang at a certain point? (The "val: -11620.7” type printouts are showing you the objective function values during the shape fitting). Since the fissure particle stage is randomly seeded, by rerunning you will get a different output that might not have the issues you are seeing.

If you see this happen again, let me know, and I can dig deeper to find out what’s going on.

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Monday, February 13, 2017 at 11:58 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi James,

I was wondering when you run the code on my data, did it finish ? It has been running for 5 hours and it is not finished yet. Using top, it show it is running FitLobeSurfaceModel. On the COPDGene data, it finished in less than an hour. This is the output so far:

/home/batmangh/MyPylon2Space/Projects/shirALI/scripts/segmentLobes.py --in_ct /home/batmangh/MyPylon2Space/LUNA16/subset0/1.3.6.1.4.1.14519.5.2.1.6279.6001.108197895896446896160048741492.mhd --out_ct /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --out_lbl /home/batmangh/MyPylon2Space/LUNA16/subset0/lbl.nrrd --out_lob /home/batmangh/MyPylon2Space/LUNA16/subset0/lob.nrrd --out_iso_ct /home/batmangh/MyPylon2Space/LUNA16/subset0/img_iso.nrrd --out_iso_lbl /home/batmangh/MyPylon2Space/LUNA16/subset0/lbl_iso.nrrd --out_iso_lob /home/batmangh/MyPylon2Space/LUNA16/subset0/lob_iso.nrrd $ /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/bin/ReadWriteImageData --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/1.3.6.1.4.1.14519.5.2.1.6279.6001.108197895896446896160048741492.mhd --oct /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd (simulated) $ /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/bin/GeneratePartialLungLabelMap --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --olm /home/batmangh/MyPylon2Space/LUNA16/subset0/lbl.nrrd (simulated) 170213-19:01:09,340 workflow INFO: ['check', 'execution', 'logging'] 170213-19:01:10,430 workflow INFO: Running serially. 170213-19:01:10,432 workflow INFO: Executing node generate_partial_lung_label_map in dir: /tmp/tmpLpSTX2/LungLobeSegmentationWorkflow/generate_partial_lung_label_map 170213-19:01:10,443 workflow INFO: Running: GeneratePartialLungLabelMap --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --olm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd 170213-19:01:13,207 interface INFO: stdout 2017-02-13T19:01:13.207733:Clipping low CT image values... 170213-19:01:13,208 interface INFO: stdout 2017-02-13T19:01:13.207733:Clipping upper CT image values... 170213-19:01:13,208 interface INFO: stdout 2017-02-13T19:01:13.207733:Executing partial lung filter... 170213-19:01:40,782 interface INFO: stdout 2017-02-13T19:01:40.782446:Writing lung mask image... 170213-19:01:41,794 interface INFO: stdout 2017-02-13T19:01:41.794386:DONE. 170213-19:01:42,338 workflow INFO: Executing node generate_lobe_surface_models in dir: /tmp/tmpFZsk4X/LungLobeSegmentationWorkflow/generate_lobe_surface_models 170213-19:01:42,355 workflow INFO: Running: GenerateLobeSurfaceModels --dir /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd --irlm /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpBAykls/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpBAykls/cid_rightLungLobesShapeModel.csv 170213-19:01:43,195 interface INFO: stdout 2017-02-13T19:01:43.195598:Read in 100 atlas resource file pairs. 170213-19:01:43,196 interface INFO: stdout 2017-02-13T19:01:43.195598:Reading fixed image... 170213-19:01:43,697 interface INFO: stdout 2017-02-13T19:01:43.697033:Subsampling fixed image... 170213-19:01:43,697 interface INFO: stdout 2017-02-13T19:01:43.697033:Reading moving image... 170213-19:01:45,219 interface INFO: stdout 2017-02-13T19:01:45.219116:Subsampling moving image... 170213-19:01:45,219 interface INFO: stdout 2017-02-13T19:01:45.219116:Extracting whole lung region from down sampled fixed image... 170213-19:01:45,219 interface INFO: stdout 2017-02-13T19:01:45.219116:Extracting whole lung region from down sampled moving image... 170213-19:01:45,219 interface INFO: stdout 2017-02-13T19:01:45.219116:Registering reference image to input image... 170213-19:01:46,741 interface INFO: stdout 2017-02-13T19:01:46.741734:Reading transform from file... 170213-19:01:46,742 interface INFO: stdout 2017-02-13T19:01:46.741734:Reading fissure points from file... 170213-19:01:47,244 interface INFO: stdout 2017-02-13T19:01:47.243377:Reading transform from file... 170213-19:01:47,244 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170213-19:01:50,262 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading transform from file... 170213-19:01:50,262 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading fissure points from file... 170213-19:01:50,262 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading transform from file... 170213-19:01:50,262 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading fissure points from file... 170213-19:01:50,262 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading transform from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading fissure points from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading transform from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading fissure points from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading transform from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading fissure points from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading transform from file... 170213-19:01:50,263 interface INFO: stdout 2017-02-13T19:01:50.261426:Reading fissure points from file... 170213-19:01:50,764 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading fissure points from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading fissure points from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading fissure points from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading fissure points from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:50,765 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading fissure points from file... 170213-19:01:50,766 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:50,766 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading fissure points from file... 170213-19:01:50,766 interface INFO: stdout 2017-02-13T19:01:50.764420:Reading transform from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,267 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,268 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,269 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,269 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading transform from file... 170213-19:01:51,269 interface INFO: stdout 2017-02-13T19:01:51.266988:Reading fissure points from file... 170213-19:01:51,770 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,770 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,770 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,770 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,770 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,771 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,772 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:51,772 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading fissure points from file... 170213-19:01:51,772 interface INFO: stdout 2017-02-13T19:01:51.769934:Reading transform from file... 170213-19:01:52,273 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,273 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,273 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,277 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,277 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,278 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading transform from file... 170213-19:01:52,279 interface INFO: stdout 2017-02-13T19:01:52.272995:Reading fissure points from file... 170213-19:01:52,780 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading transform from file... 170213-19:01:52,780 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading fissure points from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading transform from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading fissure points from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading transform from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading fissure points from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading transform from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading fissure points from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading transform from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading fissure points from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading transform from file... 170213-19:01:52,781 interface INFO: stdout 2017-02-13T19:01:52.780588:Reading fissure points from file... 170213-19:01:52,782 interface INFO: stdout 2017-02-13T19:01:52.780588:Getting range locations... 170213-19:01:55,325 interface INFO: stdout 2017-02-13T19:01:55.325200:Writing right shape model to file... 170213-19:01:55,325 interface INFO: stdout 2017-02-13T19:01:55.325200:Writing left shape model to file... 170213-19:01:55,325 interface INFO: stdout 2017-02-13T19:01:55.325200:DONE. 170213-19:01:55,861 workflow INFO: Executing node fissure_particles_node in dir: /tmp/tmp6Qol8C/LungLobeSegmentationWorkflow/fissure_particles_node Reading file for NA... Reading file for hevec1... Reading file for hevec0... Reading file for val... Reading file for hevec2... Reading file for h0... Reading file for h1... Reading file for h2... Reading file for hess... Reading file for hmode... Writing poly data... DONE. -o /tmp/tmpBAykls/cid_fissureParticles.vtk -b -i /tmp/tmpuaG81Y/pass3.nrrd -a NA -i /tmp/tmpuaG81Y/hevec1.nrrd -a hevec1 -i /tmp/tmpuaG81Y/hevec0.nrrd -a hevec0 -i /tmp/tmpuaG81Y/val.nrrd -a val -i /tmp/tmpuaG81Y/hevec2.nrrd -a hevec2 -i /tmp/tmpuaG81Y/heval0.nrrd -a h0 -i /tmp/tmpuaG81Y/heval1.nrrd -a h1 -i /tmp/tmpuaG81Y/heval2.nrrd -a h2 -i /tmp/tmpuaG81Y/hess.nrrd -a hess -i /tmp/tmpuaG81Y/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.859375,0.859375,2.5 --cipr UndefinedRegion --cipt Fissure 170213-20:10:03,787 workflow INFO: Runtime memory and threads stats unavailable 170213-20:10:03,793 workflow INFO: Executing node pre_filter_fissure_particle_data in dir: /tmp/tmpQ6pIIW/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data 170213-20:10:03,798 workflow INFO: Running: FilterFissureParticleData --dist 3.000000 --ifp /tmp/tmpBAykls/cid_fissureParticles.vtk --ofp /tmp/tmpBAykls/cid_preFilteredFissureParticles.vtk --size 110 170213-20:10:04,565 interface INFO: stdout 2017-02-13T20:10:04.565028:Reading polydata... 170213-20:10:04,566 interface INFO: stdout 2017-02-13T20:10:04.565028:Filtering particles using connectedness... 170213-20:10:08,642 interface INFO: stdout 2017-02-13T20:10:08.642286:Writing filtered particles ... 170213-20:10:08,642 interface INFO: stdout 2017-02-13T20:10:08.642286:DONE. 170213-20:10:09,179 workflow INFO: Executing node extract_left_particles in dir: /tmp/tmpNuvKxX/LungLobeSegmentationWorkflow/extract_left_particles 170213-20:10:09,188 workflow INFO: Running: ExtractParticlesFromChestRegionChestType --cipr LeftLung --ilm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd --ip /tmp/tmpBAykls/cid_preFilteredFissureParticles.vtk --op /tmp/tmpBAykls/cid_leftPreFilteredFissureParticles.vtk 170213-20:10:09,965 interface INFO: stdout 2017-02-13T20:10:09.964944:Reading polydata... 170213-20:10:09,965 interface INFO: stdout 2017-02-13T20:10:09.964944:Extracting... 170213-20:10:09,965 interface INFO: stdout 2017-02-13T20:10:09.964944:Reading label map... 170213-20:10:10,475 interface INFO: stdout 2017-02-13T20:10:10.474931:Writing extracted particles... 170213-20:10:11,487 interface INFO: stdout 2017-02-13T20:10:11.487267:DONE. 170213-20:10:12,22 workflow INFO: Executing node extract_right_particles in dir: /tmp/tmpvtivDN/LungLobeSegmentationWorkflow/extract_right_particles 170213-20:10:12,29 workflow INFO: Running: ExtractParticlesFromChestRegionChestType --cipr RightLung --ilm /tmp/tmpBAykls/cid_partialLungLabelMap.nrrd --ip /tmp/tmpBAykls/cid_preFilteredFissureParticles.vtk --op /tmp/tmpBAykls/cid_rightPreFilteredFissureParticles.vtk 170213-20:10:12,755 interface INFO: stdout 2017-02-13T20:10:12.754932:Reading polydata... 170213-20:10:12,755 interface INFO: stdout 2017-02-13T20:10:12.754932:Extracting... 170213-20:10:12,755 interface INFO: stdout 2017-02-13T20:10:12.754932:Reading label map... 170213-20:10:13,767 interface INFO: stdout 2017-02-13T20:10:13.767433:Writing extracted particles... 170213-20:10:14,779 interface INFO: stdout 2017-02-13T20:10:14.779378:DONE. 170213-20:10:15,331 workflow INFO: Executing node fit_lobe_surface_models_to_particle_data in dir: /tmp/tmpNlAabr/LungLobeSegmentationWorkflow/fit_lobe_surface_models_to_particle_data 170213-20:10:15,339 workflow INFO: Running: FitLobeSurfaceModelsToParticleData --ilfp /tmp/tmpBAykls/cid_leftPreFilteredFissureParticles.vtk --ilsm /tmp/tmpBAykls/cid_leftLungLobesShapeModel.csv --irfp /tmp/tmpBAykls/cid_rightPreFilteredFissureParticles.vtk --irsm /tmp/tmpBAykls/cid_rightLungLobesShapeModel.csv --iters 200 --olsm /tmp/tmpBAykls/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpBAykls/cid_rightLungLobesShapeModel.csv --reg 50.000000 170213-20:10:16,113 interface INFO: stdout 2017-02-13T20:10:16.112776:Reading left lung fissure particles... 170213-20:10:16,614 interface INFO: stdout 2017-02-13T20:10:16.614101:Asserting chest-region chest-type existence... 170213-20:10:16,614 interface INFO: stdout 2017-02-13T20:10:16.614101:Reading right lung fissure particles... 170213-20:10:17,625 interface INFO: stdout 2017-02-13T20:10:17.625677:Asserting chest-region chest-type existence... 170213-20:10:17,626 interface INFO: stdout 2017-02-13T20:10:17.625677:Reading left surface model... 170213-20:10:17,626 interface INFO: stdout 2017-02-13T20:10:17.625677:Fraction variance explained by modes used in left surface model: 0.992118 170213-20:10:17,626 interface INFO: stdout 2017-02-13T20:10:17.625677:Reading right surface model... 170213-20:10:17,626 interface INFO: stdout 2017-02-13T20:10:17.625677:Fraction variance explained by modes used in right surface model: 0.977813 170213-20:10:17,626 interface INFO: stdout 2017-02-13T20:10:17.625677:Executing Nelder-Mead optimizer (left lung)... 170213-20:11:25,538 interface INFO: stdout 2017-02-13T20:11:25.538208:val: -8836.71 170213-20:11:40,341 interface INFO: stdout 2017-02-13T20:11:40.341000:val: -10410.2 170213-20:11:46,458 interface INFO: stdout 2017-02-13T20:11:46.458330:val: -10410.2 170213-20:11:53,86 interface INFO: stdout 2017-02-13T20:11:53.086415:val: -10410.2 170213-20:12:07,887 interface INFO: stdout 2017-02-13T20:12:07.886989:val: -10482.6 170213-20:12:19,111 interface INFO: stdout 2017-02-13T20:12:19.111235:val: -10609.2 170213-20:12:26,250 interface INFO: stdout 2017-02-13T20:12:26.250156:val: -10609.2 170213-20:12:33,388 interface INFO: stdout 2017-02-13T20:12:33.388359:val: -10609.2 170213-20:12:46,656 interface INFO: stdout 2017-02-13T20:12:46.656392:val: -10609.2 170213-20:12:53,284 interface INFO: stdout 2017-02-13T20:12:53.284871:val: -10609.2 170213-20:13:06,551 interface INFO: stdout 2017-02-13T20:13:06.551632:val: -10609.2 170213-20:13:20,840 interface INFO: stdout 2017-02-13T20:13:20.840211:val: -10812.3 170213-20:13:37,683 interface INFO: stdout 2017-02-13T20:13:37.682908:val: -10812.3 170213-20:13:55,547 interface INFO: stdout 2017-02-13T20:13:55.547448:val: -10927.1 170213-20:14:04,220 interface INFO: stdout 2017-02-13T20:14:04.220723:val: -10927.1 170213-20:14:22,85 interface INFO: stdout 2017-02-13T20:14:22.085410:val: -10927.1 170213-20:14:29,226 interface INFO: stdout 2017-02-13T20:14:29.225944:val: -10927.1 170213-20:14:49,646 interface INFO: stdout 2017-02-13T20:14:49.646179:val: -11081.3 170213-20:14:59,340 interface INFO: stdout 2017-02-13T20:14:59.340565:val: -11081.3 170213-20:15:07,503 interface INFO: stdout 2017-02-13T20:15:07.503030:val: -11081.3 170213-20:15:24,857 interface INFO: stdout 2017-02-13T20:15:24.857508:val: -11159.6 170213-20:15:34,40 interface INFO: stdout 2017-02-13T20:15:34.040452:val: -11159.6 170213-20:15:50,885 interface INFO: stdout 2017-02-13T20:15:50.885259:val: -11159.6 170213-20:16:00,579 interface INFO: stdout 2017-02-13T20:16:00.579303:val: -11159.6 170213-20:16:07,719 interface INFO: stdout 2017-02-13T20:16:07.719192:val: -11159.6 170213-20:16:23,543 interface INFO: stdout 2017-02-13T20:16:23.542844:val: -11303.4 170213-20:16:40,388 interface INFO: stdout 2017-02-13T20:16:40.387918:val: -11303.4 170213-20:17:00,299 interface INFO: stdout 2017-02-13T20:17:00.299013:val: -11303.4 170213-20:17:16,633 interface INFO: stdout 2017-02-13T20:17:16.632838:val: -11303.4 170213-20:17:26,330 interface INFO: stdout 2017-02-13T20:17:26.330368:val: -11303.4 170213-20:17:43,175 interface INFO: stdout 2017-02-13T20:17:43.174901:val: -11303.4 170213-20:17:51,847 interface INFO: stdout 2017-02-13T20:17:51.847569:val: -11303.4 170213-20:18:08,185 interface INFO: stdout 2017-02-13T20:18:08.185015:val: -11303.4 170213-20:18:24,6 interface INFO: stdout 2017-02-13T20:18:24.006709:val: -11400.4 170213-20:18:31,657 interface INFO: stdout 2017-02-13T20:18:31.657717:val: -11400.4 170213-20:18:44,926 interface INFO: stdout 2017-02-13T20:18:44.925924:val: -11400.4 170213-20:18:52,577 interface INFO: stdout 2017-02-13T20:18:52.576903:val: -11400.4 170213-20:19:00,227 interface INFO: stdout 2017-02-13T20:19:00.227248:val: -11400.4 170213-20:19:17,74 interface INFO: stdout 2017-02-13T20:19:17.074344:val: -11400.4 170213-20:19:32,897 interface INFO: stdout 2017-02-13T20:19:32.897351:val: -11400.4 170213-20:19:39,528 interface INFO: stdout 2017-02-13T20:19:39.528565:val: -11400.4 170213-20:19:57,906 interface INFO: stdout 2017-02-13T20:19:57.906474:val: -11471.7 170213-20:20:06,578 interface INFO: stdout 2017-02-13T20:20:06.578203:val: -11471.7 170213-20:20:21,892 interface INFO: stdout 2017-02-13T20:20:21.891664:val: -11471.7 170213-20:20:36,183 interface INFO: stdout 2017-02-13T20:20:36.182505:val: -11471.7 170213-20:20:44,347 interface INFO: stdout 2017-02-13T20:20:44.347306:val: -11471.7 170213-20:20:53,20 interface INFO: stdout 2017-02-13T20:20:53.020732:val: -11471.7 170213-20:21:09,353 interface INFO: stdout 2017-02-13T20:21:09.353059:val: -11488.2 170213-20:21:17,518 interface INFO: stdout 2017-02-13T20:21:17.518187:val: -11488.2 170213-20:21:33,852 interface INFO: stdout 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[kayhan-batmanghelich]

Hi James,

It turned out that we are running the code on two different images. The image I sent you is fine. As you said, it runs smoothly and produces reasonable results. On the second image, I re-ran the code and after six hours it stopped exactly at the same step (it got killed by the scheduler because it ran out of time). When I check the top, I see FitLobeSurfaceM running. I have included the output below. If you want to run it in your system, the files are here:

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0

The filename of the image that stops is (I ran the code on the nrrd versio of this):

1.3.6.1.4.1.14519.5.2.1.6279.6001.108197895896446896160048741492.mhd 

Here is the output:

     ['check', 'execution', 'logging']
170216-11:35:16,213 workflow INFO:
     Running serially.
170216-11:35:16,214 workflow INFO:
     Executing node generate_partial_lung_label_map in dir: /tmp/tmpftuZGU/LungLobeSegmentationWorkflow/generate_partial_lung_label_map
170216-11:35:16,225 workflow INFO:
     Running:  GeneratePartialLungLabelMap  --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --olm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd
170216-11:35:27,500 interface INFO:
     stdout 2017-02-16T11:35:27.500000:Clipping low CT image values...
170216-11:35:27,500 interface INFO:
     stdout 2017-02-16T11:35:27.500000:Clipping upper CT image values...
170216-11:35:27,500 interface INFO:
     stdout 2017-02-16T11:35:27.500000:Executing partial lung filter...
170216-11:35:59,668 interface INFO:
     stdout 2017-02-16T11:35:59.667910:Writing lung mask image...
170216-11:36:00,680 interface INFO:
     stdout 2017-02-16T11:36:00.680270:DONE.
170216-11:36:01,243 workflow INFO:
     Executing node generate_lobe_surface_models in dir: /tmp/tmpd9Fn3b/LungLobeSegmentationWorkflow/generate_lobe_surface_models
170216-11:36:01,263 workflow INFO:
     Running:  GenerateLobeSurfaceModels  --dir /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd --irlm /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpQgIgfO/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpQgIgfO/cid_rightLungLobesShapeModel.csv
170216-11:36:02,194 interface INFO:
     stdout 2017-02-16T11:36:02.194487:Read in 100 atlas resource file pairs.
170216-11:36:02,195 interface INFO:
     stdout 2017-02-16T11:36:02.194487:Reading fixed image...
170216-11:36:03,206 interface INFO:
     stdout 2017-02-16T11:36:03.206738:Subsampling fixed image...
170216-11:36:03,207 interface INFO:
     stdout 2017-02-16T11:36:03.206738:Reading moving image...
170216-11:36:04,729 interface INFO:
     stdout 2017-02-16T11:36:04.729437:Subsampling moving image...
170216-11:36:04,729 interface INFO:
     stdout 2017-02-16T11:36:04.729437:Extracting whole lung region from down sampled fixed image...
170216-11:36:04,729 interface INFO:
     stdout 2017-02-16T11:36:04.729437:Extracting whole lung region from down sampled moving image...
170216-11:36:05,230 interface INFO:
     stdout 2017-02-16T11:36:05.230775:Registering reference image to input image...
170216-11:36:06,753 interface INFO:
     stdout 2017-02-16T11:36:06.753171:Reading transform from file...
170216-11:36:06,753 interface INFO:
     stdout 2017-02-16T11:36:06.753171:Reading fissure points from file...
170216-11:36:07,254 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,254 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,254 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,254 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading transform from file...
170216-11:36:07,255 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,256 interface INFO:
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170216-11:36:07,256 interface INFO:
     stdout 2017-02-16T11:36:07.254384:Reading fissure points from file...
170216-11:36:07,757 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading transform from file...
170216-11:36:07,757 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading fissure points from file...
170216-11:36:07,757 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading transform from file...
170216-11:36:07,757 interface INFO:
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170216-11:36:07,757 interface INFO:
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170216-11:36:07,757 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading fissure points from file...
170216-11:36:07,757 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading transform from file...
170216-11:36:07,757 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading fissure points from file...
170216-11:36:07,758 interface INFO:
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170216-11:36:07,758 interface INFO:
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170216-11:36:07,758 interface INFO:
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170216-11:36:07,758 interface INFO:
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170216-11:36:07,758 interface INFO:
     stdout 2017-02-16T11:36:07.756893:Reading fissure points from file...
170216-11:36:08,259 interface INFO:
     stdout 2017-02-16T11:36:08.259565:Reading transform from file...
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170216-11:36:08,260 interface INFO:
     stdout 2017-02-16T11:36:08.259565:Reading transform from file...
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     stdout 2017-02-16T11:36:08.259565:Reading fissure points from file...
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170216-11:36:08,260 interface INFO:
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170216-11:36:08,260 interface INFO:
     stdout 2017-02-16T11:36:08.259565:Reading transform from file...
170216-11:36:08,260 interface INFO:
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170216-11:36:08,260 interface INFO:
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170216-11:36:08,260 interface INFO:
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170216-11:36:08,260 interface INFO:
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170216-11:36:08,260 interface INFO:
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170216-11:36:08,261 interface INFO:
     stdout 2017-02-16T11:36:08.259565:Reading transform from file...
170216-11:36:08,261 interface INFO:
     stdout 2017-02-16T11:36:08.259565:Reading fissure points from file...
170216-11:36:08,261 interface INFO:
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170216-11:36:08,261 interface INFO:
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170216-11:36:08,261 interface INFO:
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170216-11:36:08,261 interface INFO:
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170216-11:36:08,261 interface INFO:
     stdout 2017-02-16T11:36:08.259565:Reading transform from file...
170216-11:36:08,261 interface INFO:
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170216-11:36:08,261 interface INFO:
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170216-11:36:08,261 interface INFO:
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170216-11:36:08,762 interface INFO:
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170216-11:36:08,763 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
170216-11:36:08,763 interface INFO:
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     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,763 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
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     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,763 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
170216-11:36:08,763 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,763 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
170216-11:36:08,763 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,764 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
170216-11:36:08,764 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,764 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
170216-11:36:08,764 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,764 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading fissure points from file...
170216-11:36:08,764 interface INFO:
     stdout 2017-02-16T11:36:08.762695:Reading transform from file...
170216-11:36:08,764 interface INFO:
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     stdout 2017-02-16T11:36:09.265983:Reading transform from file...
170216-11:36:09,268 interface INFO:
     stdout 2017-02-16T11:36:09.265983:Reading fissure points from file...
170216-11:36:09,268 interface INFO:
     stdout 2017-02-16T11:36:09.265983:Reading transform from file...
170216-11:36:09,268 interface INFO:
     stdout 2017-02-16T11:36:09.265983:Reading fissure points from file...
170216-11:36:09,268 interface INFO:
     stdout 2017-02-16T11:36:09.265983:Reading transform from file...
170216-11:36:09,769 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,769 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,770 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,771 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,771 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,771 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,771 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,771 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,771 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,772 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,772 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,772 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,772 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:09,772 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading fissure points from file...
170216-11:36:09,772 interface INFO:
     stdout 2017-02-16T11:36:09.769593:Reading transform from file...
170216-11:36:10,273 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,273 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,274 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,275 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,276 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,276 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading fissure points from file...
170216-11:36:10,276 interface INFO:
     stdout 2017-02-16T11:36:10.273607:Reading transform from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading transform from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading transform from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading transform from file...
170216-11:36:10,777 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:10,778 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading transform from file...
170216-11:36:10,778 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:10,778 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading transform from file...
170216-11:36:10,778 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:10,778 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading transform from file...
170216-11:36:10,778 interface INFO:
     stdout 2017-02-16T11:36:10.776989:Reading fissure points from file...
170216-11:36:11,283 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,283 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,283 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,283 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,283 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,284 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,285 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,285 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,285 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,285 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,285 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading transform from file...
170216-11:36:11,285 interface INFO:
     stdout 2017-02-16T11:36:11.282725:Reading fissure points from file...
170216-11:36:11,786 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,786 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,786 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,786 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,786 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,787 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,788 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,788 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,788 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:11,788 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading fissure points from file...
170216-11:36:11,788 interface INFO:
     stdout 2017-02-16T11:36:11.786265:Reading transform from file...
170216-11:36:12,289 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading fissure points from file...
170216-11:36:12,289 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading transform from file...
170216-11:36:12,289 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading fissure points from file...
170216-11:36:12,289 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading transform from file...
170216-11:36:12,289 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading fissure points from file...
170216-11:36:12,289 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading transform from file...
170216-11:36:12,290 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading fissure points from file...
170216-11:36:12,290 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading transform from file...
170216-11:36:12,290 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Reading fissure points from file...
170216-11:36:12,290 interface INFO:
     stdout 2017-02-16T11:36:12.289225:Getting range locations...
170216-11:36:15,344 interface INFO:
     stdout 2017-02-16T11:36:15.344477:Writing right shape model to file...
170216-11:36:15,344 interface INFO:
     stdout 2017-02-16T11:36:15.344477:Writing left shape model to file...
170216-11:36:15,344 interface INFO:
     stdout 2017-02-16T11:36:15.344477:DONE.
170216-11:36:15,881 workflow INFO:
     Executing node fissure_particles_node in dir: /tmp/tmpknGe2g/LungLobeSegmentationWorkflow/fissure_particles_node
Reading file for NA...
Reading file for hevec1...
Reading file for hevec0...
Reading file for val...
Reading file for hevec2...
Reading file for h0...
Reading file for h1...
Reading file for h2...
Reading file for hess...
Reading file for hmode...
Writing poly data...
DONE.
 -o /tmp/tmpQgIgfO/cid_fissureParticles.vtk -b -i /tmp/tmpcdfTAF/pass3.nrrd -a NA -i /tmp/tmpcdfTAF/hevec1.nrrd -a hevec1 -i /tmp/tmpcdfTAF/hevec0.nrrd -a hevec0 -i /tmp/tmpcdfTAF/val.nrrd -a val -i /tmp/tmpcdfTAF/hevec2.nrrd -a hevec2 -i /tmp/tmpcdfTAF/heval0.nrrd -a h0 -i /tmp/tmpcdfTAF/heval1.nrrd -a h1 -i /tmp/tmpcdfTAF/heval2.nrrd -a h2 -i /tmp/tmpcdfTAF/hess.nrrd -a hess -i /tmp/tmpcdfTAF/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.859375,0.859375,2.5 --cipr UndefinedRegion --cipt Fissure
170216-12:53:34,25 workflow INFO:
     Runtime memory and threads stats unavailable
170216-12:53:34,29 workflow INFO:
     Executing node pre_filter_fissure_particle_data in dir: /tmp/tmp3W8YoP/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data
170216-12:53:34,33 workflow INFO:
     Running:  FilterFissureParticleData  --dist 3.000000 --ifp /tmp/tmpQgIgfO/cid_fissureParticles.vtk --ofp /tmp/tmpQgIgfO/cid_preFilteredFissureParticles.vtk --size 110
170216-12:53:34,792 interface INFO:
     stdout 2017-02-16T12:53:34.792071:Reading polydata...
170216-12:53:34,792 interface INFO:
     stdout 2017-02-16T12:53:34.792071:Filtering particles using connectedness...
170216-12:53:38,868 interface INFO:
     stdout 2017-02-16T12:53:38.868400:Writing filtered particles ...
170216-12:53:39,369 interface INFO:
     stdout 2017-02-16T12:53:39.369507:DONE.
170216-12:53:39,902 workflow INFO:
     Executing node extract_right_particles in dir: /tmp/tmpKxA3t0/LungLobeSegmentationWorkflow/extract_right_particles
170216-12:53:39,912 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr RightLung --ilm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd --ip /tmp/tmpQgIgfO/cid_preFilteredFissureParticles.vtk --op /tmp/tmpQgIgfO/cid_rightPreFilteredFissureParticles.vtk
170216-12:53:40,644 interface INFO:
     stdout 2017-02-16T12:53:40.644717:Reading polydata...
170216-12:53:40,645 interface INFO:
     stdout 2017-02-16T12:53:40.644717:Extracting...
170216-12:53:40,645 interface INFO:
     stdout 2017-02-16T12:53:40.644717:Reading label map...
170216-12:53:41,657 interface INFO:
     stdout 2017-02-16T12:53:41.656949:Writing extracted particles...
170216-12:53:42,668 interface INFO:
     stdout 2017-02-16T12:53:42.668566:DONE.
170216-12:53:43,198 workflow INFO:
     Executing node extract_left_particles in dir: /tmp/tmp0G0Nm2/LungLobeSegmentationWorkflow/extract_left_particles
170216-12:53:43,204 workflow INFO:
     Running:  ExtractParticlesFromChestRegionChestType  --cipr LeftLung --ilm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd --ip /tmp/tmpQgIgfO/cid_preFilteredFissureParticles.vtk --op /tmp/tmpQgIgfO/cid_leftPreFilteredFissureParticles.vtk
170216-12:53:43,945 interface INFO:
     stdout 2017-02-16T12:53:43.945681:Reading polydata...
170216-12:53:43,946 interface INFO:
     stdout 2017-02-16T12:53:43.945681:Extracting...
170216-12:53:43,946 interface INFO:
     stdout 2017-02-16T12:53:43.945681:Reading label map...
170216-12:53:44,958 interface INFO:
     stdout 2017-02-16T12:53:44.957948:Writing extracted particles...
170216-12:53:45,459 interface INFO:
     stdout 2017-02-16T12:53:45.458989:DONE.
170216-12:53:45,995 workflow INFO:
     Executing node fit_lobe_surface_models_to_particle_data in dir: /tmp/tmpVz_JAO/LungLobeSegmentationWorkflow/fit_lobe_surface_models_to_particle_data
170216-12:53:46,3 workflow INFO:
     Running:  FitLobeSurfaceModelsToParticleData  --ilfp /tmp/tmpQgIgfO/cid_leftPreFilteredFissureParticles.vtk --ilsm /tmp/tmpQgIgfO/cid_leftLungLobesShapeModel.csv --irfp /tmp/tmpQgIgfO/cid_rightPreFilteredFissureParticles.vtk --irsm /tmp/tmpQgIgfO/cid_rightLungLobesShapeModel.csv --iters 200 --olsm /tmp/tmpQgIgfO/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpQgIgfO/cid_rightLungLobesShapeModel.csv --reg 50.000000
170216-12:53:46,740 interface INFO:
     stdout 2017-02-16T12:53:46.740462:Reading left lung fissure particles...
170216-12:53:47,241 interface INFO:
     stdout 2017-02-16T12:53:47.241628:Asserting chest-region chest-type existence...
170216-12:53:47,241 interface INFO:
     stdout 2017-02-16T12:53:47.241628:Reading right lung fissure particles...
170216-12:53:48,253 interface INFO:
     stdout 2017-02-16T12:53:48.253151:Asserting chest-region chest-type existence...
170216-12:53:48,253 interface INFO:
     stdout 2017-02-16T12:53:48.253151:Reading left surface model...
170216-12:53:48,253 interface INFO:
     stdout 2017-02-16T12:53:48.253151:Fraction variance explained by modes used in left surface model: 0.992118
170216-12:53:48,253 interface INFO:
     stdout 2017-02-16T12:53:48.253151:Reading right surface model...
170216-12:53:48,253 interface INFO:
     stdout 2017-02-16T12:53:48.253151:Fraction variance explained by modes used in right surface model:    0.977813
170216-12:53:48,253 interface INFO:
     stdout 2017-02-16T12:53:48.253151:Executing Nelder-Mead optimizer (left lung)...
170216-12:54:58,218 interface INFO:
     stdout 2017-02-16T12:54:58.217777:val: -8836.71
170216-12:55:13,529 interface INFO:
     stdout 2017-02-16T12:55:13.529359:val: -10410.2
170216-12:55:21,181 interface INFO:
     stdout 2017-02-16T12:55:21.180925:val: -10410.2
170216-12:55:28,321 interface INFO:
     stdout 2017-02-16T12:55:28.321036:val: -10410.2
170216-12:55:45,674 interface INFO:
     stdout 2017-02-16T12:55:45.674393:val: -10482.6
170216-12:55:59,452 interface INFO:
     stdout 2017-02-16T12:55:59.452915:val: -10609.2
170216-12:56:07,614 interface INFO:
     stdout 2017-02-16T12:56:07.614793:val: -10609.2
170216-12:56:16,286 interface INFO:
     stdout 2017-02-16T12:56:16.286292:val: -10609.2
170216-12:56:32,107 interface INFO:
     stdout 2017-02-16T12:56:32.107794:val: -10609.2
170216-12:56:39,758 interface INFO:
     stdout 2017-02-16T12:56:39.758541:val: -10609.2
170216-12:56:55,580 interface INFO:
     stdout 2017-02-16T12:56:55.579963:val: -10609.2
170216-12:57:11,911 interface INFO:
     stdout 2017-02-16T12:57:11.911371:val: -10812.3
170216-12:57:28,753 interface INFO:
     stdout 2017-02-16T12:57:28.753028:val: -10812.3
170216-12:57:45,83 interface INFO:
     stdout 2017-02-16T12:57:45.083958:val: -10927.1
170216-12:57:52,733 interface INFO:
     stdout 2017-02-16T12:57:52.733775:val: -10927.1
170216-12:58:08,44 interface INFO:
     stdout 2017-02-16T12:58:08.044698:val: -10927.1
170216-12:58:14,673 interface INFO:
     stdout 2017-02-16T12:58:14.673486:val: -10927.1
170216-12:58:32,27 interface INFO:
     stdout 2017-02-16T12:58:32.026887:val: -11081.3
170216-12:58:40,699 interface INFO:
     stdout 2017-02-16T12:58:40.699007:val: -11081.3
170216-12:58:48,859 interface INFO:
     stdout 2017-02-16T12:58:48.859883:val: -11081.3
170216-12:59:03,658 interface INFO:
     stdout 2017-02-16T12:59:03.658901:val: -11159.6
170216-12:59:12,331 interface INFO:
     stdout 2017-02-16T12:59:12.331166:val: -11159.6
170216-12:59:27,131 interface INFO:
     stdout 2017-02-16T12:59:27.131104:val: -11159.6
170216-12:59:35,802 interface INFO:
     stdout 2017-02-16T12:59:35.802504:val: -11159.6
170216-12:59:42,943 interface INFO:
     stdout 2017-02-16T12:59:42.943394:val: -11159.6
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[kayhan-batmanghelich]

It seems Nelder-Mead optimizer stops somewhere.

[kayhan-batmanghelich]

Another thing that I found is that the workflow creates LungLobeSegmentationWorkflow in the data folder. So if there are multiple jobs concurrently running on multiple images at the same folder (that is what I am doing), there will be writing race. Am I missing something? Can we have LungLobeSegmentationWorkflow in the temp folder?

[jcross186]

Hi Kayhan,

The algorithm finished on my machine for this case, although the result (esp. in the right lung) is not very good. This case is quite challenging — the fissures are quite faint. For very challenging cases like this, you can use the Interactive Lobe Segmentation Module in the CIP Slicer extension. You could also try running vessel particles for this case and passing those to the lobe segmentation workflow. But if you only have a handful of problem cases, I recommend using the interactive tool.

Hth,

-James

From: Kayhan Batmanghelich notifications@github.com<mailto:notifications@github.com> Reply-To: acil-bwh/ChestImagingPlatform reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, February 16, 2017 at 5:46 PM To: acil-bwh/ChestImagingPlatform ChestImagingPlatform@noreply.github.com<mailto:ChestImagingPlatform@noreply.github.com> Cc: James Ross jross@bwh.harvard.edu<mailto:jross@bwh.harvard.edu>, Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [acil-bwh/ChestImagingPlatform] probably bug in the lung_lobe_segmentation_workflow.py (#14)

Hi James,

It turned out that we are running the code on two different images. The image I sent you is fine. As you said, it runs smoothly and produces reasonable results. On the second image, the code runs six hours it stopped exactly at the same step (it got killed by the scheduler because it ran out of time). When I check the top, I see FitLobeSurfaceM running. I have included the output below. If you want to run it in your system, the files are here:

https://www.dropbox.com/sh/x6qmvi4jgfmvkk6/AABnp-wDU1IMfsiY4XKyDgXKa?dl=0

The filename of the image that stops is (I ran the code on the nrrd versio of this):

1.3.6.1.4.1.14519.5.2.1.6279.6001.108197895896446896160048741492.mhd

Here is the output:

     ['check', 'execution', 'logging']

170216-11:35:16,213 workflow INFO: Running serially. 170216-11:35:16,214 workflow INFO: Executing node generate_partial_lung_label_map in dir: /tmp/tmpftuZGU/LungLobeSegmentationWorkflow/generate_partial_lung_label_map 170216-11:35:16,225 workflow INFO: Running: GeneratePartialLungLabelMap --ict /home/batmangh/MyPylon2Space/LUNA16/subset0/img.nrrd --olm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd 170216-11:35:27,500 interface INFO: stdout 2017-02-16T11:35:27.500000:Clipping low CT image values... 170216-11:35:27,500 interface INFO: stdout 2017-02-16T11:35:27.500000:Clipping upper CT image values... 170216-11:35:27,500 interface INFO: stdout 2017-02-16T11:35:27.500000:Executing partial lung filter... 170216-11:35:59,668 interface INFO: stdout 2017-02-16T11:35:59.667910:Writing lung mask image... 170216-11:36:00,680 interface INFO: stdout 2017-02-16T11:36:00.680270:DONE. 170216-11:36:01,243 workflow INFO: Executing node generate_lobe_surface_models in dir: /tmp/tmpd9Fn3b/LungLobeSegmentationWorkflow/generate_lobe_surface_models 170216-11:36:01,263 workflow INFO: Running: GenerateLobeSurfaceModels --dir /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/ --ilm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd --irlm /home/batmangh/MyPylon2Space/installed/ChestImagingPlatform/CIP-build/cip_python/nipype/workflows/../../../Resources/LungLobeAtlasData/10002K_INSP_STD_BWH_COPD_leftLungRightLung.nrrd --olsm /tmp/tmpQgIgfO/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpQgIgfO/cid_rightLungLobesShapeModel.csv 170216-11:36:02,194 interface INFO: stdout 2017-02-16T11:36:02.194487:Read in 100 atlas resource file pairs. 170216-11:36:02,195 interface INFO: stdout 2017-02-16T11:36:02.194487:Reading fixed image... 170216-11:36:03,206 interface INFO: stdout 2017-02-16T11:36:03.206738:Subsampling fixed image... 170216-11:36:03,207 interface INFO: stdout 2017-02-16T11:36:03.206738:Reading moving image... 170216-11:36:04,729 interface INFO: stdout 2017-02-16T11:36:04.729437:Subsampling moving image... 170216-11:36:04,729 interface INFO: stdout 2017-02-16T11:36:04.729437:Extracting whole lung region from down sampled fixed image... 170216-11:36:04,729 interface INFO: stdout 2017-02-16T11:36:04.729437:Extracting whole lung region from down sampled moving image... 170216-11:36:05,230 interface INFO: stdout 2017-02-16T11:36:05.230775:Registering reference image to input image... 170216-11:36:06,753 interface INFO: stdout 2017-02-16T11:36:06.753171:Reading transform from file... 170216-11:36:06,753 interface INFO: stdout 2017-02-16T11:36:06.753171:Reading fissure points from file... 170216-11:36:07,254 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading transform from file... 170216-11:36:07,254 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading fissure points from file... 170216-11:36:07,254 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading transform from file... 170216-11:36:07,254 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading fissure points from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading transform from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading fissure points from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading transform from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading fissure points from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading transform from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading fissure points from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading transform from file... 170216-11:36:07,255 interface INFO: stdout 2017-02-16T11:36:07.254384:Reading fissure points from file... 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170216-11:36:08,261 interface INFO: stdout 2017-02-16T11:36:08.259565:Reading transform from file... 170216-11:36:08,261 interface INFO: stdout 2017-02-16T11:36:08.259565:Reading fissure points from file... 170216-11:36:08,762 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading transform from file... 170216-11:36:08,763 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading fissure points from file... 170216-11:36:08,763 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading transform from file... 170216-11:36:08,763 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading fissure points from file... 170216-11:36:08,763 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading transform from file... 170216-11:36:08,763 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading fissure points from file... 170216-11:36:08,763 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading transform from file... 170216-11:36:08,763 interface INFO: stdout 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170216-11:36:08,764 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading fissure points from file... 170216-11:36:08,764 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading transform from file... 170216-11:36:08,765 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading fissure points from file... 170216-11:36:08,765 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading transform from file... 170216-11:36:08,765 interface INFO: stdout 2017-02-16T11:36:08.762695:Reading fissure points from file... 170216-11:36:09,266 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,266 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,266 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,266 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,267 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,268 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,268 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,268 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,268 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,268 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading fissure points from file... 170216-11:36:09,268 interface INFO: stdout 2017-02-16T11:36:09.265983:Reading transform from file... 170216-11:36:09,769 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,769 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,770 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,771 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,771 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,771 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,771 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,771 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,771 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,772 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,772 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,772 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,772 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:09,772 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading fissure points from file... 170216-11:36:09,772 interface INFO: stdout 2017-02-16T11:36:09.769593:Reading transform from file... 170216-11:36:10,273 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,273 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,274 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,275 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,276 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,276 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading fissure points from file... 170216-11:36:10,276 interface INFO: stdout 2017-02-16T11:36:10.273607:Reading transform from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading transform from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading transform from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading transform from file... 170216-11:36:10,777 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:10,778 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading transform from file... 170216-11:36:10,778 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:10,778 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading transform from file... 170216-11:36:10,778 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:10,778 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading transform from file... 170216-11:36:10,778 interface INFO: stdout 2017-02-16T11:36:10.776989:Reading fissure points from file... 170216-11:36:11,283 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,283 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,283 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,283 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,283 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,284 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,285 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,285 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,285 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,285 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,285 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading transform from file... 170216-11:36:11,285 interface INFO: stdout 2017-02-16T11:36:11.282725:Reading fissure points from file... 170216-11:36:11,786 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,786 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,786 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,786 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,786 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,787 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,788 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,788 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,788 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:11,788 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading fissure points from file... 170216-11:36:11,788 interface INFO: stdout 2017-02-16T11:36:11.786265:Reading transform from file... 170216-11:36:12,289 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading fissure points from file... 170216-11:36:12,289 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading transform from file... 170216-11:36:12,289 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading fissure points from file... 170216-11:36:12,289 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading transform from file... 170216-11:36:12,289 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading fissure points from file... 170216-11:36:12,289 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading transform from file... 170216-11:36:12,290 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading fissure points from file... 170216-11:36:12,290 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading transform from file... 170216-11:36:12,290 interface INFO: stdout 2017-02-16T11:36:12.289225:Reading fissure points from file... 170216-11:36:12,290 interface INFO: stdout 2017-02-16T11:36:12.289225:Getting range locations... 170216-11:36:15,344 interface INFO: stdout 2017-02-16T11:36:15.344477:Writing right shape model to file... 170216-11:36:15,344 interface INFO: stdout 2017-02-16T11:36:15.344477:Writing left shape model to file... 170216-11:36:15,344 interface INFO: stdout 2017-02-16T11:36:15.344477:DONE. 170216-11:36:15,881 workflow INFO: Executing node fissure_particles_node in dir: /tmp/tmpknGe2g/LungLobeSegmentationWorkflow/fissure_particles_node Reading file for NA... Reading file for hevec1... Reading file for hevec0... Reading file for val... Reading file for hevec2... Reading file for h0... Reading file for h1... Reading file for h2... Reading file for hess... Reading file for hmode... Writing poly data... DONE. -o /tmp/tmpQgIgfO/cid_fissureParticles.vtk -b -i /tmp/tmpcdfTAF/pass3.nrrd -a NA -i /tmp/tmpcdfTAF/hevec1.nrrd -a hevec1 -i /tmp/tmpcdfTAF/hevec0.nrrd -a hevec0 -i /tmp/tmpcdfTAF/val.nrrd -a val -i /tmp/tmpcdfTAF/hevec2.nrrd -a hevec2 -i /tmp/tmpcdfTAF/heval0.nrrd -a h0 -i /tmp/tmpcdfTAF/heval1.nrrd -a h1 -i /tmp/tmpcdfTAF/heval2.nrrd -a h2 -i /tmp/tmpcdfTAF/hess.nrrd -a hess -i /tmp/tmpcdfTAF/hmode.nrrd -a hmode --irad 1.7 --srad 1.2 --liveth -15.0 --seedth -45.0 --spacing 0.859375,0.859375,2.5 --cipr UndefinedRegion --cipt Fissure 170216-12:53:34,25 workflow INFO: Runtime memory and threads stats unavailable 170216-12:53:34,29 workflow INFO: Executing node pre_filter_fissure_particle_data in dir: /tmp/tmp3W8YoP/LungLobeSegmentationWorkflow/pre_filter_fissure_particle_data 170216-12:53:34,33 workflow INFO: Running: FilterFissureParticleData --dist 3.000000 --ifp /tmp/tmpQgIgfO/cid_fissureParticles.vtk --ofp /tmp/tmpQgIgfO/cid_preFilteredFissureParticles.vtk --size 110 170216-12:53:34,792 interface INFO: stdout 2017-02-16T12:53:34.792071:Reading polydata... 170216-12:53:34,792 interface INFO: stdout 2017-02-16T12:53:34.792071:Filtering particles using connectedness... 170216-12:53:38,868 interface INFO: stdout 2017-02-16T12:53:38.868400:Writing filtered particles ... 170216-12:53:39,369 interface INFO: stdout 2017-02-16T12:53:39.369507:DONE. 170216-12:53:39,902 workflow INFO: Executing node extract_right_particles in dir: /tmp/tmpKxA3t0/LungLobeSegmentationWorkflow/extract_right_particles 170216-12:53:39,912 workflow INFO: Running: ExtractParticlesFromChestRegionChestType --cipr RightLung --ilm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd --ip /tmp/tmpQgIgfO/cid_preFilteredFissureParticles.vtk --op /tmp/tmpQgIgfO/cid_rightPreFilteredFissureParticles.vtk 170216-12:53:40,644 interface INFO: stdout 2017-02-16T12:53:40.644717:Reading polydata... 170216-12:53:40,645 interface INFO: stdout 2017-02-16T12:53:40.644717:Extracting... 170216-12:53:40,645 interface INFO: stdout 2017-02-16T12:53:40.644717:Reading label map... 170216-12:53:41,657 interface INFO: stdout 2017-02-16T12:53:41.656949:Writing extracted particles... 170216-12:53:42,668 interface INFO: stdout 2017-02-16T12:53:42.668566:DONE. 170216-12:53:43,198 workflow INFO: Executing node extract_left_particles in dir: /tmp/tmp0G0Nm2/LungLobeSegmentationWorkflow/extract_left_particles 170216-12:53:43,204 workflow INFO: Running: ExtractParticlesFromChestRegionChestType --cipr LeftLung --ilm /tmp/tmpQgIgfO/cid_partialLungLabelMap.nrrd --ip /tmp/tmpQgIgfO/cid_preFilteredFissureParticles.vtk --op /tmp/tmpQgIgfO/cid_leftPreFilteredFissureParticles.vtk 170216-12:53:43,945 interface INFO: stdout 2017-02-16T12:53:43.945681:Reading polydata... 170216-12:53:43,946 interface INFO: stdout 2017-02-16T12:53:43.945681:Extracting... 170216-12:53:43,946 interface INFO: stdout 2017-02-16T12:53:43.945681:Reading label map... 170216-12:53:44,958 interface INFO: stdout 2017-02-16T12:53:44.957948:Writing extracted particles... 170216-12:53:45,459 interface INFO: stdout 2017-02-16T12:53:45.458989:DONE. 170216-12:53:45,995 workflow INFO: Executing node fit_lobe_surface_models_to_particle_data in dir: /tmp/tmpVz_JAO/LungLobeSegmentationWorkflow/fit_lobe_surface_models_to_particle_data 170216-12:53:46,3 workflow INFO: Running: FitLobeSurfaceModelsToParticleData --ilfp /tmp/tmpQgIgfO/cid_leftPreFilteredFissureParticles.vtk --ilsm /tmp/tmpQgIgfO/cid_leftLungLobesShapeModel.csv --irfp /tmp/tmpQgIgfO/cid_rightPreFilteredFissureParticles.vtk --irsm /tmp/tmpQgIgfO/cid_rightLungLobesShapeModel.csv --iters 200 --olsm /tmp/tmpQgIgfO/cid_leftLungLobesShapeModel.csv --orsm /tmp/tmpQgIgfO/cid_rightLungLobesShapeModel.csv --reg 50.000000 170216-12:53:46,740 interface INFO: stdout 2017-02-16T12:53:46.740462:Reading left lung fissure particles... 170216-12:53:47,241 interface INFO: stdout 2017-02-16T12:53:47.241628:Asserting chest-region chest-type existence... 170216-12:53:47,241 interface INFO: stdout 2017-02-16T12:53:47.241628:Reading right lung fissure particles... 170216-12:53:48,253 interface INFO: stdout 2017-02-16T12:53:48.253151:Asserting chest-region chest-type existence... 170216-12:53:48,253 interface INFO: stdout 2017-02-16T12:53:48.253151:Reading left surface model... 170216-12:53:48,253 interface INFO: stdout 2017-02-16T12:53:48.253151:Fraction variance explained by modes used in left surface model: 0.992118 170216-12:53:48,253 interface INFO: stdout 2017-02-16T12:53:48.253151:Reading right surface model... 170216-12:53:48,253 interface INFO: stdout 2017-02-16T12:53:48.253151:Fraction variance explained by modes used in right surface model: 0.977813 170216-12:53:48,253 interface INFO: stdout 2017-02-16T12:53:48.253151:Executing Nelder-Mead optimizer (left lung)... 170216-12:54:58,218 interface INFO: stdout 2017-02-16T12:54:58.217777:val: -8836.71 170216-12:55:13,529 interface INFO: stdout 2017-02-16T12:55:13.529359:val: 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[kiwixiao]

Hi Kayhan Does you add path method working? I am having same issues and add path does not solve the problem.