search

nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
297 stars 132 forks source link

Failure of workflow: Bias.a0 #357

Closed angoldst closed 7 years ago

angoldst commented 7 years ago

Thanks again for the help.

Crash report:

File: /share/leanew1/MKET_Study/MKET_BIDS_data_test/out/logs/crash-20170202-073924-agoldpie-Bias.a0-d4e7d498-f9f2-45de-ae88-29ae6975ebb6.pklz
Node: workflow_enumerator.anatMRIQC.Bias.a0
Working directory: /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/Bias

Node inputs:

args = <undefined>
bias_image = <undefined>
bspline_fitting_distance = <undefined>
bspline_order = <undefined>
convergence_threshold = <undefined>
dimension = 3
environ = {u'NSLOTS': u'1'}
ignore_exception = False
input_image = /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii
mask_image = <undefined>
n_iterations = <undefined>
num_threads = 1
output_image = <undefined>
save_bias = True
shrink_factor = <undefined>
terminal_output = stream
weight_image = <undefined>

Traceback: 
Traceback (most recent call last):
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 52, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 366, in run
    self._run_interface()
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 476, in _run_interface
    self._result = self._run_command(execute)
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 607, in _run_command
    result = self._interface.run()
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1086, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1180, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: File/Directory '/share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/Bias/sub-346228_ses-baseline_T1w_conformed_corrected.nii' not found for N4BiasFieldCorrection output 'output_image'.
Interface N4BiasFieldCorrection failed to run.

In looking at the actual output from the script I also get this:

Description: itk::ERROR: Image(0x2b77cf0): A spacing of 0 is not allowed: Spacing is [0]
Standard error:

Return code: 1
Interface Registration failed to run. .
170202-07:40:07,270 niworkflows INFO:
     Loading settings from file /home/agoldpie/anaconda2/lib/python2.7/site-packages/niworkflows/data/epi-mni_registration_001.json.
170202-07:40:07,275 niworkflows INFO:
     Retry #1, commandline: 
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/MNIApplyMask/2mm_T2_masked.nii.gz, /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..func..sub-346228_ses-baseline_task-rest_bold.nii/EPIApplyMask/sub-346228_ses-baseline_task-rest_bold_mcf_tstat_corrected_masked.nii.gz, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ epi_to_mni, epi_to_mni_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric Mattes[ /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/MNIApplyMask/2mm_T2_masked.nii.gz, /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..func..sub-346228_ses-baseline_task-rest_bold.nii/EPIApplyMask/sub-346228_ses-baseline_task-rest_bold_mcf_tstat_corrected_masked.nii.gz, 1, 56, Random, 0.8 ] --convergence [ 10000, 1e-07, 250 ] --smoothing-sigmas 8.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/MNIApplyMask/2mm_T2_masked.nii.gz, /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..func..sub-346228_ses-baseline_task-rest_bold.nii/EPIApplyMask/sub-346228_ses-baseline_task-rest_bold_mcf_tstat_corrected_masked.nii.gz, 1, 32, Random, 0.3 ] --convergence [ 100, 1e-08, 5 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.01 ] --metric Mattes[ /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/MNIApplyMask/2mm_T2_masked.nii.gz, /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..func..sub-346228_ses-baseline_task-rest_bold.nii/EPIApplyMask/sub-346228_ses-baseline_task-rest_bold_mcf_tstat_corrected_masked.nii.gz, 1, 32, Random, 0.25 ] --convergence [ 10000, 1e-08, 500 ] --smoothing-sigmas 1.0vox --shrink-factors 2 --use-estimate-learning-rate-once 0 --use-histogram-matching 1 --winsorize-image-intensities [ 0.01, 0.9995 ]  --write-composite-transform 0

system/pip details for reference

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.5 LTS"
NAME="Ubuntu"
VERSION="14.04.5 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.5 LTS"
VERSION_ID="14.04"
anaconda-client==1.4.0
anaconda-navigator==1.2.1
argcomplete==1.0.0
astropy==1.2.1
Babel==2.3.3
backports-abc==0.4
backports.shutil-get-terminal-size==1.0.0
backports.ssl-match-hostname==3.4.0.2
beautifulsoup4==4.4.1
bitarray==0.8.1
blaze==0.10.1
bokeh==0.12.0
boto==2.40.0
Bottleneck==1.1.0
cdecimal==2.3
cffi==1.6.0
chest==0.2.3
click==6.6
cloudpickle==0.2.1
clyent==1.2.2
colorama==0.3.7
conda==4.2.13
conda-build==1.21.3
configobj==5.0.6
configparser==3.5.0b2
contextlib2==0.5.3
cryptography==1.4
cycler==0.10.0
Cython==0.24
cytoolz==0.8.0
dask==0.10.0
datashape==0.5.2
decorator==4.0.10
dill==0.2.5
dipy==0.11.0
docutils==0.12
dynd==0.7.3.dev1
enum34==1.1.6
et-xmlfile==1.0.1
fastcache==1.0.2
Flask==0.11.1
Flask-Cors==2.1.2
funcsigs==1.0.2
functools32==3.2.3.post2
future==0.16.0
futures==3.0.5
gevent==1.1.1
grabbit==0.0.5.1
greenlet==0.4.10
grin==1.2.1
h5py==2.6.0
HeapDict==1.0.0
html5lib==0.999999999
idna==2.1
imagesize==0.7.1
ipaddress==1.0.16
ipykernel==4.3.1
ipython==4.2.0
ipython-genutils==0.1.0
ipywidgets==4.1.1
isodate==0.5.4
itsdangerous==0.24
jdcal==1.2
jedi==0.9.0
Jinja2==2.8
jsonschema==2.5.1
jupyter==1.0.0
jupyter-client==4.3.0
jupyter-console==4.1.1
jupyter-core==4.1.0
llvmlite==0.11.0
locket==0.2.0
lxml==3.6.0
MarkupSafe==0.23
matplotlib==1.5.1
mistune==0.7.2
mock==2.0.0
mpmath==0.19
mriqc==0.9.0rc1
multipledispatch==0.4.8
nb-anacondacloud==1.1.0
nb-conda==1.1.0
nb-conda-kernels==1.0.3
nbconvert==4.2.0
nbformat==4.0.1
nbpresent==3.0.2
networkx==1.11
nibabel==2.1.0
nilearn==0.2.6
nipy==0.4.0
nipype==0.13.0rc1
nitime==0.7
niworkflows==0.0.5
nltk==3.2.1
nose==1.3.7
notebook==4.2.1
numba==0.26.0
numexpr==2.6.0
numpy==1.11.1
odo==0.5.0
openpyxl==2.3.2
pandas==0.18.1
partd==0.3.4
path.py==0.0.0
pathlib2==2.1.0
patsy==0.4.1
pbr==1.10.0
pep8==1.7.0
pexpect==4.0.1
pickleshare==0.7.2
Pillow==3.2.0
ply==3.8
prov==1.5.0
psutil==4.3.0
ptyprocess==0.5.1
py==1.4.31
pyasn1==0.1.9
pybids==0.0.1
pycairo==1.10.0
pycosat==0.6.1
pycparser==2.14
pycrypto==2.6.1
pycurl==7.43.0
pydicom==0.9.9
pydotplus==2.0.2
pyflakes==1.2.3
Pygments==2.1.3
pyOpenSSL==16.2.0
pyparsing==2.1.4
pytest==3.0.6
python-dateutil==2.5.3
pytz==2016.4
PyYAML==3.11
pyzmq==15.2.0
qtconsole==4.2.1
QtPy==1.0.2
rdflib==4.2.1
redis==2.10.5
requests==2.12.4
rope==0.9.4
scikit-image==0.12.3
scikit-learn==0.17.1
scipy==0.17.1
seaborn==0.7.1
simplegeneric==0.8.1
simplejson==3.10.0
singledispatch==3.4.0.3
six==1.10.0
sklearn==0.0
snowballstemmer==1.2.1
sockjs-tornado==1.0.3
SPARQLWrapper==1.8.0
Sphinx==1.4.1
sphinx-rtd-theme==0.1.9
spyder==2.3.9
SQLAlchemy==1.0.13
statsmodels==0.6.1
svgutils==0.2.0
sympy==1.0
tables==3.2.2
terminado==0.6
tinycss==0.4
toolz==0.8.0
tornado==4.3
traitlets==4.2.1
traits==4.6.0
unicodecsv==0.14.1
webencodings==0.5
Werkzeug==0.11.10
xlrd==1.0.0
XlsxWriter==0.9.2
xlwt==1.1.2
xvfbwrapper==0.2.9
oesteban commented 7 years ago

Could you post the output of:

nib-ls /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii

Or, if nib-ls is not available to you:

fslinfo /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii
angoldst commented 7 years ago

Thank you Oscar. On my way into lab now via public transit will hopefully be able to do this in about 2 hours.

Sent from my iPhone

On Feb 2, 2017, at 08:40, Oscar Esteban notifications@github.com<mailto:notifications@github.com> wrote:

Could you post the output of:

nib-ls /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_infile..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii

Or, if nib-ls is not available to you:

fslinfo /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_infile..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/poldracklab/mriqc/issues/357#issuecomment-277010446, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFGGsTcboF8wlBczi22gqpq_CI9qeRlSks5rYgcHgaJpZM4L1R0Y.

angoldst commented 7 years ago

Sorry for the delay, today is always swamped with meetings. Tried running it again after resolving the numpy issue for the computDVARS.

Now get this error for the Bias:

Node: workflow_enumerator.anatMRIQC.Bias.a0
Working directory: /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/Bias

Node inputs:

args = <undefined>
bias_image = <undefined>
bspline_fitting_distance = <undefined>
bspline_order = <undefined>
convergence_threshold = <undefined>
dimension = 3
environ = {u'NSLOTS': u'1'}
ignore_exception = False
input_image = /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii
mask_image = <undefined>
n_iterations = <undefined>
num_threads = 1
output_image = <undefined>
save_bias = True
shrink_factor = <undefined>
terminal_output = stream
weight_image = <undefined>

Traceback: 
Traceback (most recent call last):
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 52, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 366, in run
    self._run_interface()
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 476, in _run_interface
    self._result = self._run_command(execute)
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 607, in _run_command
    result = self._interface.run()
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1086, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/agoldpie/anaconda2/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1180, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: File/Directory '/share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/Bias/sub-346228_ses-baseline_T1w_conformed_corrected.nii' not found for N4BiasFieldCorrection output 'output_image'.
Interface N4BiasFieldCorrection failed to run.

Here is the other file info you requested:

agoldpie@sni-vcs-williams:~$ fslinfo /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform/sub-346228_ses-baseline_T1w_conformed.nii
data_type      UINT16
dim1           256
dim2           256
dim3           176
dim4           1
datatype       512
pixdim1        0.976600
pixdim2        0.976600
pixdim3        1.000002
pixdim4        0.000000
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+

Thanks again.

oesteban commented 7 years ago

could you (careful with this rm, I don't take responsibilities for it :)

rm -r /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_in_file_..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform

And re-run to see if there is some problem related to numpy arrays? The error of the spacing being 0 is pretty weird, especially after checking your fslinfo.

angoldst commented 7 years ago

Yeah definitely I can try again once I get home. I had deleted all of the work and files prior to rerunning it this last time. Will be back at my computer in 2 hours.

Sent from my iPhone

On Feb 2, 2017, at 16:05, Oscar Esteban notifications@github.com<mailto:notifications@github.com> wrote:

could you

rm -r /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_infile..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform

And re-run to see if there is some problem related to numpy arrays? The error of the spacing being 0 is pretty weird, especially after checking your fslinfo.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/poldracklab/mriqc/issues/357#issuecomment-277125325, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFGGsX7cOWjCdYHeHz6BFDZfC_qjKUgGks5rYm8_gaJpZM4L1R0Y.

chrisgorgo commented 7 years ago

I think the spacing thing is unrelated. It's coming from the robust mni interface. I run into it with another subject that run to completion without errors.

On Feb 2, 2017 7:05 PM, "Oscar Esteban" notifications@github.com wrote:

could you

rm -r /share/leanew1/MKET_Study/MKET_BIDS_data_test/work/workflow_enumerator/anatMRIQC/_infile..share..leanew1..MKET_Study..MKET_BIDS_data_test..sub-346228..ses-baseline..anat..sub-346228_ses-baseline_T1w.nii/conform

And re-run to see if there is some problem related to numpy arrays? The error of the spacing being 0 is pretty weird, especially after checking your fslinfo.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/poldracklab/mriqc/issues/357#issuecomment-277125325, or mute the thread https://github.com/notifications/unsubscribe-auth/AAOkpzHYzlwjkPVwmETqsInYqGhZrs9lks5rYm8_gaJpZM4L1R0Y .

angoldst commented 7 years ago

This looks to be resolved as well with a new download of ants.

Thanks again.