Scinet quarantine: nii2mnc

[raihaan]

Had an issue running nii2mnc using updated module setup, but was able to run nii2mnc on same file using minc-tools/mice-chihiro

Old style:

gpc-f102n084-ib0-$ module list
Currently Loaded Modulefiles:
  1) quarantine                     3) gcc/4.6.1                      5) intel/12.1.3                   7) python/2.7.2                   9) gotoblas/1.13-singlethreaded  11) /minc-tools/mice-chihiro
  2) gnu-parallel/20140622          4) nano/2.2.4                     6) extras/64_6.4                  8) gnuplot/4.6.1                 10) openmpi/1.4.4-intel-v12.1
gpc-f102n084-ib0-$ nii2mnc AA2006D211Dy1_T1.nii test.mnc
<nifti_image
  nifti_type = 'NIFTI-1+'
  header_filename = 'AA2006D211Dy1_T1.nii'
  image_filename = 'AA2006D211Dy1_T1.nii'
  image_offset = '352'
  ndim = '3'
  nx = '256'
  ny = '256'
  nz = '124'
  dx = '0.7813'
  dy = '0.7813'
  dz = '1.5'
  datatype = '4'
  datatype_name = 'INT16'
  nvox = '8126464'
  nbyper = '2'
  byteorder = 'LSB_FIRST'
  scl_slope = '1'
  scl_inter = '0'
  xyz_units = '2'
  xyz_units_name = 'mm'
  time_units = '8'
  time_units_name = 's'
  descrip = 'FSL5.0'
  aux_file = 'E2801S2I1.MR'
  num_ext = '0'
/>
xspace start: -100.0064 step:   0.7813 cosines:   1.0000   0.0000   0.0000
yspace start: -100.0064 step:   0.7813 cosines:   0.0000   1.0000   0.0000
zspace start: -93.0000 step:   1.5000 cosines:   0.0000   0.0000   1.0000
gpc-f102n084-ib0-$ ls test.mnc 
test.mnc
gpc-f102n084-ib0-$ mincinfo test.mnc 
file: test.mnc
image: signed__ short 0 to 2253
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                    124          1.5          -93
    yspace                    256       0.7813     -100.006
    xspace                    256       0.7813     -100.006

Meanwhile:

scinet01-ib0-$ gpcdev
ssh  gpc02 
Last login: Wed Jul 29 13:16:11 2015 from scinet01
gpc-f102n084-ib0-$ module list
No Modulefiles Currently Loaded.
gpc-f102n084-ib0-$ module use -a /project/m/mchakrav/quarantine/modules/
gpc-f102n084-ib0-$ module load scinet
gpc-f102n084-ib0-$ module list
Currently Loaded Modulefiles:
  1) /quarantine                              6) gnu-parallel/20140622                   11) ImageMagick/6.9.1-4                     16) /bpipe/0.9.8.7
  2) gcc/4.9.0                                7) mesa/7.11                               12) /minc-toolkit/1.9.10                    17) /scinet
  3) intel/15.0.2                             8) python/2.7.8                            13) /pyminc/0.41
  4) git/1.9.5                                9) extras/64_6.4                           14) /minc-stuffs/0.1.9^minc-toolkit-1.9.10
  5) nano/2.2.4                              10) Xlibraries/X11-64                       15) java/oracle-java-x86_64-80_45
gpc-f102n084-ib0-$ cd scratch/
gpc-f102n084-ib0-$ nii2mnc AA2006D211Dy1_T1.nii new.mnc
<nifti_image
  nifti_type = 'NIFTI-1+'
  header_filename = 'AA2006D211Dy1_T1.nii'
  image_filename = 'AA2006D211Dy1_T1.nii'
  image_offset = '352'
  ndim = '3'
  nx = '256'
  ny = '256'
  nz = '124'
  dx = '0.7813'
  dy = '0.7813'
  dz = '1.5'
  datatype = '4'
  datatype_name = 'INT16'
  nvox = '8126464'
  nbyper = '2'
  byteorder = 'LSB_FIRST'
  scl_slope = '1'
  scl_inter = '0'
  xyz_units = '2'
  xyz_units_name = 'mm'
  time_units = '8'
  time_units_name = 's'
  descrip = 'FSL5.0'
  aux_file = 'E2801S2I1.MR'
  num_ext = '0'
/>
Segmentation fault
gpc-f102n084-ib0-$ ls new.mnc
ls: cannot access new.mnc: No such file or directory

[raihaan]

I tried to convert /scratch/m/mchakrav/patelmo6/AA2006D211Dy1_T1.nii

/scratch/m/mchakrav/patelmo6/test.mnc was the output from nii2mnc using chihiro

[gdevenyi]

Some .nii files are awful and broken, nii2mnc doesn't like them.

itk_convert can do it

[gdevenyi]

If an example file is available to share, I can submit a bug upstream to @vfonov

[vfonov]

There were changes to mnc2nii and nii2mnc : https://github.com/BIC-MNI/minc-tools/commits/develop/conversion/nifti1 , maybe you happen to have different versions on different systems?

[gdevenyi]

@vfonov The failing version is from minc-toolkit-1.9.10, the succeeding version is from a much older version from the MICe quarantine builder

1.9.10 fails on both SciNet and at the CIC here (one built on ICC on scinet, one built on debian 6.0 gcc)

[vfonov]

can you give me the .nii file that causes the crash?

[gdevenyi]

@vfonov Waiting on @raihaan to get permission from the original owner of the file so we can share.