========[ 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