200116-19:53:00,198 nipype.workflow INFO: Generated workflow graph: /output_dir/nipype/sub-01/anatomical_pipeline/graph.svg (graph2use=colored, simple_form=True). 200116-19:53:00,200 nipype.interface INFO: **** Processing **** 200116-19:53:00,400 nipype.workflow INFO: Workflow anatomical_pipeline settings: ['check', 'execution', 'logging', 'monitoring'] 200116-19:53:00,500 nipype.workflow INFO: Running serially. 200116-19:53:00,502 nipype.workflow INFO: [Node] Setting-up "anatomical_pipeline.datasource" in "/output_dir/nipype/sub-01/anatomical_pipeline/datasource". 200116-19:53:00,532 nipype.workflow INFO: [Node] Running "datasource" ("nipype.interfaces.io.DataGrabber") 200116-19:53:00,591 nipype.workflow INFO: [Node] Finished "anatomical_pipeline.datasource". 200116-19:53:00,594 nipype.workflow INFO: [Node] Setting-up "anatomical_pipeline.segmentation_stage.mgz_convert" in "/output_dir/nipype/sub-01/anatomical_pipeline/segmentation_stage/mgz_convert". 200116-19:53:00,643 nipype.workflow INFO: [Node] Running "mgz_convert" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command: mri_convert --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_desc-cmp_T1w.nii.gz --output_volume T1.mgz 200116-19:53:01,347 nipype.interface INFO: stdout 2020-01-16T19:53:01.347786:mri_convert.bin --out_type mgz --resample_type interpolate -voxsize 1.000000 1.000000 1.000000 --input_volume /output_dir/cmp/sub-01/anat/sub-01_desc-cmp_T1w.nii.gz --output_volume T1.mgz 200116-19:53:06,852 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ 200116-19:53:06,867 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:reading from /output_dir/cmp/sub-01/anat/sub-01_desc-cmp_T1w.nii.gz... 200116-19:53:06,868 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:TR=1850.00, TE=0.00, TI=0.00, flip angle=0.00 200116-19:53:06,870 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:i_ras = (-1, 0, 0) 200116-19:53:06,871 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:j_ras = (0, 1, 0) 200116-19:53:06,872 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:k_ras = (0, 0, 1) 200116-19:53:06,873 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:Reslicing using trilinear interpolation 200116-19:53:06,875 nipype.interface INFO: stdout 2020-01-16T19:53:06.852125:writing to T1.mgz... 200116-19:53:06,983 nipype.workflow INFO: [Node] Finished "anatomical_pipeline.segmentation_stage.mgz_convert". 200116-19:53:06,986 nipype.workflow INFO: [Node] Setting-up "anatomical_pipeline.segmentation_stage.copy_orig" in "/output_dir/nipype/sub-01/anatomical_pipeline/segmentation_stage/copy_orig". 200116-19:53:07,28 nipype.workflow INFO: [Node] Running "copy_orig" ("nipype.interfaces.utility.base.Rename") 200116-19:53:07,114 nipype.workflow INFO: [Node] Finished "anatomical_pipeline.segmentation_stage.copy_orig". 200116-19:53:07,116 nipype.workflow INFO: [Node] Setting-up "anatomical_pipeline.segmentation_stage.reconall" in "/output_dir/nipype/sub-01/anatomical_pipeline/segmentation_stage/reconall". 200116-19:53:07,299 nipype.interface INFO: recon-all complete : Not running 200116-19:53:07,306 nipype.workflow INFO: [Node] Running "reconall" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 200116-19:53:07,456 nipype.interface INFO: recon-all complete : Not running 200116-19:53:07,942 nipype.interface INFO: stdout 2020-01-16T19:53:07.942047:recon-all: nothing to do 200116-19:53:09,724 nipype.workflow INFO: [Node] Finished "anatomical_pipeline.segmentation_stage.reconall". 200116-19:53:09,727 nipype.workflow INFO: [Node] Setting-up "anatomical_pipeline.parcellation_stage.Lausanne2018_parcellation" in "/output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/Lausanne2018_parcellation". 200116-19:53:10,4 nipype.workflow INFO: [Node] Running "Lausanne2018_parcellation" ("cmtklib.parcellation.Parcellate") 200116-19:53:10,7 nipype.interface INFO: --------------------------------------------------------------------------------------- 200116-19:53:10,8 nipype.interface INFO: ROI_HR_th.nii.gz / fsmask_1mm.nii.gz CREATION (Parcellation scheme : Lausanne2018) 200116-19:53:10,10 nipype.interface INFO: --------------------------------------------------------------------------------------- 200116-19:53:12,911 nipype.interface INFO: > Create aparc+aseg.nii.gz in native space as /output_dir/freesurfer/sub-01/tmp/aparc+aseg.native.nii.gz 200116-19:53:12,912 nipype.interface INFO: ... Command: mri_vol2vol --mov "/output_dir/freesurfer/sub-01/mri/aparc+aseg.mgz" --targ "/output_dir/freesurfer/sub-01/mri/rawavg.mgz" --regheader --o "/output_dir/freesurfer/sub-01/tmp/aparc+aseg.native.nii.gz" --no-save-reg --interp nearest 200116-19:53:14,731 nipype.interface INFO: [DONE] 200116-19:53:14,732 nipype.interface INFO: Generate LAUSANNE2018 MULTISCALE PARCELLATION for input subject sub-01 200116-19:53:14,735 nipype.interface INFO: * FreeSurfer subjects directory ($SUBJECTS_DIR): /output_dir/freesurfer 200116-19:53:14,737 nipype.interface INFO: * FreeSurfer subjects directory ($SUBJECTS_DIR) DOES contain 'fsaverage' 200116-19:53:14,740 nipype.interface INFO: * Freesurfer subject directory: /output_dir/freesurfer/sub-01 (subject id: sub-01) 200116-19:53:14,742 nipype.interface INFO: Copy fsaverage 200116-19:53:14,750 nipype.interface INFO: ... Working on multiscale parcellation, SCALE 1 200116-19:53:14,752 nipype.interface INFO: > Resample fsaverage CorticalSurface to individual CorticalSurface 200116-19:53:28,284 nipype.interface INFO: > Generate Nifti volume from annotation 200116-19:56:27,110 nipype.interface INFO: > Relabel cortical and subcortical regions 200116-19:56:27,440 nipype.interface INFO: > Save output volumes 200116-19:56:29,494 nipype.interface INFO: ... Working on multiscale parcellation, SCALE 2 200116-19:56:29,497 nipype.interface INFO: > Resample fsaverage CorticalSurface to individual CorticalSurface 200116-19:56:42,69 nipype.interface INFO: > Generate Nifti volume from annotation 200116-19:59:53,584 nipype.interface INFO: > Relabel cortical and subcortical regions 200116-19:59:53,935 nipype.interface INFO: > Save output volumes 200116-19:59:55,831 nipype.interface INFO: ... Working on multiscale parcellation, SCALE 3 200116-19:59:55,833 nipype.interface INFO: > Resample fsaverage CorticalSurface to individual CorticalSurface 200116-20:00:08,404 nipype.interface INFO: > Generate Nifti volume from annotation 200116-20:03:16,445 nipype.interface INFO: > Relabel cortical and subcortical regions 200116-20:03:16,771 nipype.interface INFO: > Save output volumes 200116-20:03:18,665 nipype.interface INFO: ... Working on multiscale parcellation, SCALE 4 200116-20:03:18,667 nipype.interface INFO: > Resample fsaverage CorticalSurface to individual CorticalSurface 200116-20:03:31,138 nipype.interface INFO: > Generate Nifti volume from annotation 200116-20:06:35,577 nipype.interface INFO: > Relabel cortical and subcortical regions 200116-20:06:35,900 nipype.interface INFO: > Save output volumes 200116-20:06:37,773 nipype.interface INFO: ... Working on multiscale parcellation, SCALE 5 200116-20:06:37,775 nipype.interface INFO: > Resample fsaverage CorticalSurface to individual CorticalSurface 200116-20:06:50,314 nipype.interface INFO: > Generate Nifti volume from annotation 200116-20:09:58,34 nipype.interface INFO: > Relabel cortical and subcortical regions 200116-20:09:58,360 nipype.interface INFO: > Save output volumes 200116-20:10:00,433 nipype.interface INFO: Convert ribbon.mgz to compressed nifti 200116-20:10:01,440 nipype.interface INFO: [ DONE ] 200116-20:10:01,442 nipype.interface INFO: > Create white matter mask 200116-20:10:01,443 nipype.interface INFO: ... FreeSurfer dir: /output_dir/freesurfer/sub-01 200116-20:10:01,445 nipype.interface INFO: > load ribbon 200116-20:10:01,560 nipype.interface INFO: > Extract right and left wm 200116-20:10:02,290 nipype.interface INFO: > Load aseg 200116-20:10:02,571 nipype.interface INFO: > Ventricle erosion 200116-20:10:03,12 nipype.interface INFO: > Save CSF mask 200116-20:10:07,978 nipype.interface INFO: > Grey nuclei, either with or without erosion 200116-20:10:13,801 nipype.interface INFO: > Remove remaining structure, e.g. brainstem 200116-20:10:14,261 nipype.interface INFO: > Removing lateral ventricles and eroded grey nuclei and brainstem from white matter mask 200116-20:10:14,264 nipype.interface INFO: > Save white matter mask: /output_dir/freesurfer/sub-01/mri/fsmask_1mm.nii.gz 200116-20:10:14,675 nipype.interface INFO: > Save gray matter mask: /output_dir/freesurfer/sub-01/mri/gmmask.nii.gz 200116-20:10:20,323 nipype.interface INFO: > Cropping and moving created images 200116-20:10:20,325 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/aseg.nii.gz: 200116-20:10:22,356 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/ribbon.nii.gz: 200116-20:10:23,827 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/fsmask_1mm.nii.gz: 200116-20:10:25,808 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/gmmask.nii.gz: 200116-20:10:28,197 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/ROIv_scale4.nii.gz: 200116-20:10:30,704 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/ROIv_scale5.nii.gz: 200116-20:10:32,772 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/ROIv_scale1.nii.gz: 200116-20:10:34,819 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/ROIv_scale2.nii.gz: 200116-20:10:36,855 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/ROIv_scale3.nii.gz: 200116-20:10:38,868 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/aparc+aseg.mgz: 200116-20:10:40,968 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/brainmask.nii.gz: 200116-20:10:42,941 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/T1.nii.gz: 200116-20:10:49,995 nipype.interface INFO: ... Processing /output_dir/freesurfer/sub-01/mri/brain.nii.gz: 200116-20:10:57,294 nipype.workflow INFO: [Node] Finished "anatomical_pipeline.parcellation_stage.Lausanne2018_parcellation". 200116-20:10:57,297 nipype.workflow INFO: [Node] Setting-up "anatomical_pipeline.parcellation_stage.parcCombiner" in "/output_dir/nipype/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner". 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