Processing /output_dir/freesurfer/sub-01/mri/ROIv_scale4.nii.gz:
200115-14:10:49,530 nipype.workflow WARNING:
[Node] Error on "anatomical_pipeline.parcellation_stage.Lausanne2018_parcellation" (/output_dir/cmp/sub-01/tmp/anatomical_pipeline/parcellation_stage/Lausanne2018_parcellation)
200115-14:10:49,559 nipype.workflow ERROR:
Node Lausanne2018_parcellation failed to run on host e4589b50fe0c.
200115-14:10:49,563 nipype.workflow ERROR:
Saving crash info to /app/crash-20200115-141049-root-Lausanne2018_parcellation-0f4a5c54-3bdc-402a-ab3b-50f120efe26d.txt
Traceback (most recent call last):
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 511, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python2.7/site-packages/cmtklib/parcellation.py", line 1506, in _run_interface
crop_and_move_datasets(self.inputs.parcellation_scheme,self.inputs.subject_id, self.inputs.subjects_dir)
File "/opt/conda/lib/python2.7/site-packages/cmtklib/parcellation.py", line 2704, in crop_and_move_datasets
raise Exception('File %s does not exist.' % d[0])
Exception: File /output_dir/freesurfer/sub-01/mri/ROIv_scale4.nii.gz does not exist.
Traceback (most recent call last):
File "/opt/conda/bin/multiscalebrainparcellator", line 102, in <module>
anat_pipeline.process()
File "/opt/conda/lib/python2.7/site-packages/cmp/multiscalebrainparcellator/pipelines/anatomical/anatomical.py", line 464, in process
anat_flow.run()
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 511, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python2.7/site-packages/cmtklib/parcellation.py", line 1506, in _run_interface
crop_and_move_datasets(self.inputs.parcellation_scheme,self.inputs.subject_id, self.inputs.subjects_dir)
File "/opt/conda/lib/python2.7/site-packages/cmtklib/parcellation.py", line 2704, in crop_and_move_datasets
raise Exception('File %s does not exist.' % d[0])
Exception: File /output_dir/freesurfer/sub-01/mri/ROIv_scale4.nii.gz does not exist.
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$ docker pull sebastientourbier/multiscalebrainparcellator:v1.1.0-hotfix
$ docker images
$ docker rmi ad91fad1e8d9
docker images
)docker run -it --rm \
-v /tmp/data/ds005:/bids_dir \
-v /tmp/ds005/derivatives:/output_dir \
-v $FS_LICENSE:/bids_dir/code/license.txt \
sebastientourbier/multiscalebrainparcellator:v1.1.0-hotfix
\
/bids_dir /output_dir participant --participant_label 01 \
--isotropic_resolution 1.0 \
--thalamic_nuclei \
--hippocampal_subfields \
--brainstem_structures \
--fs_license /bids_dir/code/license.txt \
--skip_bids_validator
docker run -it --rm \
-v $parent_dir:/bids_dir \
-v $out_dir:/output_dir \
-v $FREESURFER_HOME/license.txt:/bids_dir/code/license.txt \
sebastientourbier/multiscalebrainparcellator:v1.1.0-hotfix
\
/bids_dir /output_dir participant --participant_label 01 \
--isotropic_resolution 1.0 \
--fs_license /bids_dir/code/license.txt \
--skip_bids_validator
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200116-20:10:57,667 nipype.workflow INFO:
[Node] Running "parcCombiner" ("cmtklib.parcellation.CombineParcellations")
200116-20:10:57,670 nipype.interface INFO:
------------------------------------------------------------
200116-20:10:57,671 nipype.interface INFO:
Combination of Lausanne2008 parcellation with new structures
200116-20:10:57,673 nipype.interface INFO:
------------------------------------------------------------
200116-20:10:57,674 nipype.interface INFO:
> Freesurfer subject directory: /output_dir/freesurfer/sub-01
200116-20:10:57,695 nipype.workflow WARNING:
[Node] Error on "anatomical_pipeline.parcellation_stage.parcCombiner" (/output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner)
200116-20:10:57,725 nipype.workflow ERROR:
Node parcCombiner failed to run on host 738e9cb131ba.
200116-20:10:57,756 nipype.workflow ERROR:
Saving crash info to /app/crash-20200116-201057-root-parcCombiner-60621ba1-ba0c-46e5-9736-ff69c4164381.txt
Traceback (most recent call last):
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
node.run(updatehash=updatehash)
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 369, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/py27msbparc/lib/python2.7/site-packages/cmtklib/parcellation.py", line 439, in _run_interface
iflogger.info(bcolors.WARNING + ' Subfields image (Left hemisphere) not provided' + bcolors.ENDC)
NameError: global name 'bcolors' is not defined
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