An error in MRIQC

mriqc

#1

I wish I could give this topic a more informative title, but I cannot even tell what the error is.

We are trying to process the dataset kindly made available on OpenNeuro by Dupre et al: https://openneuro.org/datasets/ds000210/versions/00002

The error message is below. If you continue scrolling you’ll see all the crash reports for the same subject (#01).

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  tr = func_nii.get_header().get_zooms()[-1]
/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nibabel/nifti1.py:582: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  ext_def = np.fromstring(ext_def, dtype=np.int32)
/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nibabel/nifti1.py:582: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
  ext_def = np.fromstring(ext_def, dtype=np.int32)
/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/matplotlib/pyplot.py:514: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  max_open_warning, RuntimeWarning)
Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/bin/mriqc", line 11, in <module>
    sys.exit(main())
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/mriqc/bin/mriqc_run.py", line 250, in main
    mriqc_wf.run(**plugin_settings)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run
    report_nodes_not_run(notrun)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

PS: well, the forum won’t let post the error message because it has >32k characters. Will post piecemeal below.


#2
========[ crash-20181206-064149-winkleram-fsl_bet.a0-7f978e7e-d5fa-4aa7-a455-72a07c26f9e1.txt ]========
Node: workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/fsl_bet

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = <undefined>
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/inu_n4/sub-01_T1w_conformed_corrected.nii.gz
mask = <undefined>
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = True
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/inu_n4/sub-01_T1w_conformed_corrected.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/fsl_bet/sub-01_T1w_conformed_corrected_brain.nii.gz -A
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w/inu_n4/sub-01_T1w_conformed_corrected
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/inu_n4/sub-01_T1w_conformed_corrected
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w/inu_n4/sub-01_T1w_conformed_corrected
Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/inu_n4/sub-01_T1w_conformed_corrected
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w/inu_n4/sub-01_T1w_conformed_corrected
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w/inu_n4/sub-01_T1w_conformed_corrected
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/inu_n4/sub-01_T1w_conformed_corrected
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w/inu_n4/sub-01_T1w_conformed_corrected
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/inu_n4/sub-01_T1w_conformed_corrected
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w/inu_n4/sub-01_T1w_conformed_corrected
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 52320 Aborted                 ${FSLDIR}/bin/bet2 $IN $OUT -e $bet2opts
error opening file
could not open the following file: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/fsl_bet/sub-01_T1w_conformed_corrected_brain_mesh.vtk
terminating.
Return code: 0
========[ crash-20181206-064939-winkleram-binarize.a0-27a3090c-906d-4e6d-b473-d25b2cbe6969.txt ]========
Node: workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/binarize

Node inputs:

args = -bin
direction = below
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/sstrip_orig_vol/sub-01_T1w_conformed_calc.nii.gz
internal_datatype = <undefined>
nan2zeros = <undefined>
out_file = <undefined>
output_datatype = <undefined>
output_type = NIFTI_GZ
thresh = 0.001
use_nonzero_voxels = <undefined>
use_robust_range = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 898, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
fslmaths /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/sstrip_orig_vol/sub-01_T1w_conformed_calc.nii.gz -thr 0.0010000000 -bin /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.nii.gz/binarize/sub-01_T1w_conformed_calc_thresh.nii.gz
Standard output:

Standard error:
terminate called after throwing an instance of 'NiftiException'
  what():  Error: cant open file /lscratch/14921106/01.wrk/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..anat..sub-01_T1w.gz/binarize/sub-01_T1w_conformed_calc_thresh.nii.gz
Return code: -6
========[ crash-20181206-065602-winkleram-bet_msk.a14-5a9450e1-39eb-4744-bd5b-2607a64ab257.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold.nii.gz/mean/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold.nii.gz/mean/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/mean/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/mean/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 53393 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/bet_msk/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 53395 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/mean/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-3_bold/mean/sub-01_task-rest_run-01_echo-3_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 53397 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0

#3
========[ crash-20181206-070224-winkleram-bet_msk.a13-3303a6d5-f7de-44c2-9ace-53c11e5ec484.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold.nii.gz/mean/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold.nii.gz/mean/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/mean/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/mean/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 54013 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/bet_msk/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 54015 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/mean/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-2_bold/mean/sub-01_task-rest_run-01_echo-2_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 54017 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-070846-winkleram-bet_msk.a12-83cf1c71-246d-48fd-bf2f-ac5125eda189.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold.nii.gz/mean/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold.nii.gz/mean/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/mean/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/mean/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold.nii.gz/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 54634 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/bet_msk/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 54636 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/mean/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-rest_run-01_echo-1_bold/mean/sub-01_task-rest_run-01_echo-1_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 54638 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-071405-winkleram-bet_msk.a11-fb49b844-7950-4060-81b0-01a7a9be31ef.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/mean/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/mean/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 55328 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 55330 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/mean/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-3_bold/mean/sub-01_task-cuedSGT_run-04_echo-3_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 55333 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0

#4
========[ crash-20181206-071921-winkleram-bet_msk.a10-9909ce68-7b91-4a22-8776-7fc4f271a137.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/mean/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/mean/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 55922 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 55924 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/mean/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-2_bold/mean/sub-01_task-cuedSGT_run-04_echo-2_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 55926 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-072437-winkleram-bet_msk.a09-8fc2b292-5231-4432-b0d6-6406b9d6e2e0.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/mean/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/mean/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 56504 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 56506 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/mean/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-04_echo-1_bold/mean/sub-01_task-cuedSGT_run-04_echo-1_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 56508 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-072953-winkleram-bet_msk.a08-a807c559-7877-4698-ad46-3af437368d9b.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/mean/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/mean/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 57092 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 57094 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/mean/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-3_bold/mean/sub-01_task-cuedSGT_run-03_echo-3_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393: 57096 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-073509-winkleram-bet_msk.a07-d0988803-bdf9-4ff4-903e-a11e964b23ef.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/mean/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/mean/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:   638 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:   640 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/mean/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-2_bold/mean/sub-01_task-cuedSGT_run-03_echo-2_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:   642 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0

#5
========[ crash-20181206-074025-winkleram-bet_msk.a06-5a352df2-bd67-40ba-a01e-70b436731255.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/mean/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/mean/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  1226 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  1228 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/mean/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-03_echo-1_bold/mean/sub-01_task-cuedSGT_run-03_echo-1_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  1230 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-074549-winkleram-bet_msk.a05-5bec7e40-eb33-4fe3-9e34-9a881074168a.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/mean/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/mean/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  3082 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  3084 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/mean/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-3_bold/mean/sub-01_task-cuedSGT_run-02_echo-3_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  3086 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-075117-winkleram-bet_msk.a04-a608c403-2a03-433b-b3fe-0073bd286367.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/mean/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/mean/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  3709 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  3711 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/mean/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-2_bold/mean/sub-01_task-cuedSGT_run-02_echo-2_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  3713 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-075646-winkleram-bet_msk.a03-a4bc700e-1b9e-4d99-a4d0-2c22e1a77c7b.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/mean/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/mean/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  4309 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  4311 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/mean/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-02_echo-1_bold/mean/sub-01_task-cuedSGT_run-02_echo-1_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  4313 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0

#6
========[ crash-20181206-080217-winkleram-bet_msk.a02-3a7f3f8d-8977-40f9-8892-27073e79c240.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold.nii.gz/mean/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/mean/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/mean/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  4988 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  4990 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/mean/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-3_bold/mean/sub-01_task-cuedSGT_run-01_echo-3_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  4992 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-080747-winkleram-bet_msk.a01-3bfbcf55-433b-48f2-a301-42be601554e7.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold.nii.gz/mean/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/mean/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/mean/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  5657 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  5659 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/mean/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-2_bold/mean/sub-01_task-cuedSGT_run-01_echo-2_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  5661 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0
========[ crash-20181206-081311-winkleram-bet_msk.a00-0db6b3c2-fb33-487b-95ef-34a05d7cf4a6.txt ]========
Node: workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk
Working directory: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold.nii.gz/bet_msk

Node inputs:

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = True
in_file = /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat.nii.gz
mask = True
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
threshold = <undefined>
vertical_gradient = <undefined>

Traceback (most recent call last):
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 511, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/fsl/preprocess.py", line 144, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs6/users/EDB/ME/code/env-hpc/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 835, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
bet /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold.nii.gz/mean/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat.nii.gz /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain.nii.gz -F -m
Standard output:

Standard error:
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/mean/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat
No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/mean/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
Image Exception : #22 :: Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
terminate called after throwing an instance of 'armawrap::AWException'
  what():  Failed to read volume /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold.nii.gz/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
Error : No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  6322 Aborted                 ${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/bet_msk/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat_brain_tmp_brain_mask
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  6324 Aborted                 ${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
Image Exception : #63 :: No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/mean/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat
terminate called after throwing an instance of 'armawrap::AWException'
  what():  No image files match: /lscratch/14921106/01.wrk/workflow_enumerator/funcMRIQC/_in_file_..gpfs..gsfs6..users..EDB..ME..BIDS..sub-01..func..sub-01_task-cuedSGT_run-01_echo-1_bold/mean/sub-01_task-cuedSGT_run-01_echo-1_bold_valid_volreg_tstat
/usr/local/apps/fsl/6.0.0/bin/bet: line 393:  6326 Aborted                 ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
Return code: 0

#7

Please note that all the above is the crash for 1 subject only.


#8

Hi @winkler,

I seems that some FSL tools are not opening files some NIfTI files. It could be a problem of the filesystem (we have recently seen some of these errors on our HPC) or, most probably, some issue with the FSL version you are using (6.0.0). I’ll try to get FSL 6.0.0 installed tomorrow. If you could share that subject with me it would be very helpful.

Other than that, at first sight, it seems like downgrading FSL to 5.0.9 (which is what we use in our automated tests) may solve the issue.

Please let me know if you would be able to get me some data to crash MRIQC.

Best,
Oscar


#9

Hi Oscar,
Many thanks. It worked just fine after downgrading to FSL 5.0.11 (which we have installed still), so it must be some incompatibility with FSL 6.
Thanks!
All the best,
Anderson