Thanks so much for your input! I changed the lines in the configuration file exactly as you suggested, but am unfortunately running into additional issues.
Looking at the log file, it seems that CMP3 is actually trying to run recon-all, which suggests to me perhaps that it failed to recognize the existing FreeSurfer derivatives. This recon-all call, however, crashes prematurely due to an error related to Perl. I'm pasting below the full contents of a log file for one subject for illustration. I'm also including the output shown in the terminal, although there is no error displayed there. I'm using v3.0.0-RC3. I'm experiencing these issues both on a macOS v10.14.5 (via Docker) and on CentOS7 (via a singularity version of the same image).
Connectome Mapper v3.0.0-RC3
Copyright (C) 2009-2021, Ecole Polytechnique Federale de Lausanne (EPFL)
the University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland,
& Contributors
All rights reserved.
INFO : No detected session
>> Load anatomical config file : /output_dir/cmp/sub-100206/sub-100206_anatomical_config.ini
**** Check Inputs ****
> Looking in /bids_dir for....
/bids_dir/sub-100206/anat/sub-100206_run-01_T1w.nii.gz
... t1_file : /bids_dir/sub-100206/anat/sub-100206_run-01_T1w.nii.gz
/bids_dir/sub-100206/anat/sub-100206_run-01_T1w.json
... t1_json_file : /bids_dir/sub-100206/anat/sub-100206_run-01_T1w.json
Inputs check finished successfully.
Only anatomical data (T1) available.
--- Set Freesurfer and ANTs to use 1 threads by the means of OpenMP
210302-15:40:47,503 nipype.interface INFO:
**** Processing ****
Freesurfer_subjects_dir: /output_dir/freesurfer
Freesurfer_subject_id: /output_dir/freesurfer/sub-100206
210302-15:40:49,725 nipype.workflow INFO:
Generated workflow graph: /output_dir/nipype/sub-100206/anatomical_pipeline/graph.svg (graph2use=colored, simple_form=True).
210302-15:40:49,940 nipype.workflow INFO:
Workflow anatomical_pipeline settings: ['check', 'execution', 'logging', 'monitoring']
210302-15:40:50,77 nipype.workflow INFO:
Running serially.
210302-15:40:50,82 nipype.workflow INFO:
[Node] Setting-up "anatomical_pipeline.datasource" in "/output_dir/nipype/sub-100206/anatomical_pipeline/datasource".
210302-15:40:50,284 nipype.workflow INFO:
[Node] Running "datasource" ("nipype.interfaces.io.DataGrabber")
210302-15:40:50,352 nipype.workflow INFO:
[Node] Finished "anatomical_pipeline.datasource".
210302-15:40:50,356 nipype.workflow INFO:
[Node] Setting-up "anatomical_pipeline.segmentation_stage.mgzConvert" in "/output_dir/nipype/sub-100206/anatomical_pipeline/segmentation_stage/mgzConvert".
210302-15:40:50,414 nipype.workflow INFO:
[Node] Cached "anatomical_pipeline.segmentation_stage.mgzConvert" - collecting precomputed outputs
210302-15:40:50,417 nipype.workflow INFO:
[Node] "anatomical_pipeline.segmentation_stage.mgzConvert" found cached.
210302-15:40:50,420 nipype.workflow INFO:
[Node] Setting-up "anatomical_pipeline.segmentation_stage.copyOrig" in "/output_dir/nipype/sub-100206/anatomical_pipeline/segmentation_stage/copyOrig".
210302-15:40:50,472 nipype.workflow INFO:
[Node] Outdated cache found for "anatomical_pipeline.segmentation_stage.copyOrig".
210302-15:40:50,736 nipype.workflow INFO:
[Node] Running "copyOrig" ("nipype.interfaces.utility.base.Rename")
210302-15:40:50,851 nipype.workflow INFO:
[Node] Finished "anatomical_pipeline.segmentation_stage.copyOrig".
210302-15:40:50,856 nipype.workflow INFO:
[Node] Setting-up "anatomical_pipeline.segmentation_stage.reconall" in "/output_dir/nipype/sub-100206/anatomical_pipeline/segmentation_stage/reconall".
210302-15:40:51,814 nipype.interface INFO:
resume recon-all : recon-all -all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-100206 -sd /output_dir/freesurfer -nomotioncor -notalairach -nonuintensitycor -nonormalization -noskullstrip -nogcareg -nocanorm -nocareg -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nosmooth2 -noinflate2 -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortribbon
210302-15:40:51,907 nipype.workflow INFO:
[Node] Running "reconall" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-100206 -sd /output_dir/freesurfer -nomotioncor -notalairach -nonuintensitycor -nonormalization -noskullstrip -nogcareg -nocanorm -nocareg -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nosmooth2 -noinflate2 -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortribbon
210302-15:40:51,999 nipype.interface INFO:
resume recon-all : recon-all -all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-100206 -sd /output_dir/freesurfer -nomotioncor -notalairach -nonuintensitycor -nonormalization -noskullstrip -nogcareg -nocanorm -nocareg -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nosmooth2 -noinflate2 -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortribbon
210302-15:40:52,417 nipype.interface INFO:
stdout 2021-03-02T15:40:52.417202:Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
210302-15:40:52,421 nipype.interface INFO:
stdout 2021-03-02T15:40:52.417202:Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
210302-15:40:52,484 nipype.interface INFO:
stdout 2021-03-02T15:40:52.484594:INFO: SUBJECTS_DIR is /output_dir/freesurfer
210302-15:40:52,490 nipype.interface INFO:
stdout 2021-03-02T15:40:52.490654:Actual FREESURFER_HOME /opt/freesurfer
210302-15:40:52,667 nipype.interface INFO:
stdout 2021-03-02T15:40:52.667158:-rwxrwxrwx 1 503 dialout 416822 Mar 2 15:32 /output_dir/freesurfer/sub-100206/scripts/recon-all.log
210302-15:40:52,714 nipype.interface INFO:
stdout 2021-03-02T15:40:52.714196:Linux 065c02599775 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
210302-15:40:52,908 nipype.interface INFO:
stderr 2021-03-02T15:40:52.908065:Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /opt/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/MiscUtilities.pm line 36.
210302-15:40:52,912 nipype.interface INFO:
stderr 2021-03-02T15:40:52.908065:BEGIN failed--compilation aborted at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/MiscUtilities.pm line 36.
210302-15:40:52,915 nipype.interface INFO:
stderr 2021-03-02T15:40:52.908065:Compilation failed in require at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/Spawn.pm line 35.
210302-15:40:52,918 nipype.interface INFO:
stderr 2021-03-02T15:40:52.908065:BEGIN failed--compilation aborted at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/Spawn.pm line 35.
210302-15:40:52,926 nipype.interface INFO:
stderr 2021-03-02T15:40:52.908065:Compilation failed in require at /opt/freesurfer/mni/bin/nu_correct line 38.
210302-15:40:52,929 nipype.interface INFO:
stderr 2021-03-02T15:40:52.908065:BEGIN failed--compilation aborted at /opt/freesurfer/mni/bin/nu_correct line 38.
210302-15:40:53,674 nipype.interface INFO:
stdout 2021-03-02T15:40:53.674913:'/opt/freesurfer/bin/recon-all' -> '/output_dir/freesurfer/sub-100206/scripts/recon-all.local-copy'
210302-15:40:53,702 nipype.interface INFO:
stdout 2021-03-02T15:40:53.702507:#--------------------------------------------
210302-15:40:53,720 nipype.interface INFO:
stdout 2021-03-02T15:40:53.720910:#@# Make White Surf lh Tue Mar 2 15:40:53 UTC 2021
210302-15:40:53,735 nipype.interface INFO:
stdout 2021-03-02T15:40:53.734976:/output_dir/freesurfer/sub-100206/scripts
210302-15:40:53,758 nipype.interface INFO:
stdout 2021-03-02T15:40:53.758118:
210302-15:40:53,762 nipype.interface INFO:
stdout 2021-03-02T15:40:53.758118: mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs sub-100206 lh
210302-15:40:53,765 nipype.interface INFO:
stdout 2021-03-02T15:40:53.758118:
210302-15:40:53,889 nipype.interface INFO:
stdout 2021-03-02T15:40:53.889729:#--------------------------------------------
210302-15:40:53,911 nipype.interface INFO:
stdout 2021-03-02T15:40:53.911058:#@# Make White Surf rh Tue Mar 2 15:40:53 UTC 2021
210302-15:40:53,921 nipype.interface INFO:
stdout 2021-03-02T15:40:53.921328:/output_dir/freesurfer/sub-100206/scripts
210302-15:40:53,945 nipype.interface INFO:
stdout 2021-03-02T15:40:53.945306:
210302-15:40:53,950 nipype.interface INFO:
stdout 2021-03-02T15:40:53.945306: mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs sub-100206 rh
210302-15:40:53,952 nipype.interface INFO:
stdout 2021-03-02T15:40:53.945306:
210302-15:40:54,193 nipype.interface INFO:
stdout 2021-03-02T15:40:54.193002:Waiting for PID 228 of (228 231) to complete...
210302-15:40:57,494 nipype.interface INFO:
stdout 2021-03-02T15:40:57.494358:Waiting for PID 231 of (228 231) to complete...
210302-15:40:57,525 nipype.interface INFO:
stdout 2021-03-02T15:40:57.525428:PIDs (228 231) completed and logs appended.
210302-15:40:57,551 nipype.interface INFO:
stdout 2021-03-02T15:40:57.551899:Linux 065c02599775 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
210302-15:40:57,561 nipype.interface INFO:
stdout 2021-03-02T15:40:57.561291:
210302-15:40:57,573 nipype.interface INFO:
stdout 2021-03-02T15:40:57.573205:recon-all -s sub-100206 exited with ERRORS at Tue Mar 2 15:40:57 UTC 2021
210302-15:40:57,582 nipype.interface INFO:
stdout 2021-03-02T15:40:57.582226:
210302-15:40:57,586 nipype.interface INFO:
stdout 2021-03-02T15:40:57.586519:For more details, see the log file /output_dir/freesurfer/sub-100206/scripts/recon-all.log
210302-15:40:57,593 nipype.interface INFO:
stdout 2021-03-02T15:40:57.593041:To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting210302-15:40:57,597 nipype.interface INFO:
stdout 2021-03-02T15:40:57.597321:
210302-15:40:57,795 nipype.workflow WARNING:
Storing result file without outputs
210302-15:40:57,832 nipype.workflow WARNING:
[Node] Error on "anatomical_pipeline.segmentation_stage.reconall" (/output_dir/nipype/sub-100206/anatomical_pipeline/segmentation_stage/reconall)
210302-15:40:57,852 nipype.workflow ERROR:
Node reconall failed to run on host 065c02599775.
210302-15:40:57,856 nipype.workflow ERROR:
Saving crash info to /tmp/crash-20210302-154057-UID503-reconall-2e8c00f4-5740-4522-8ba4-18bf69cd0634.txt
Traceback (most recent call last):
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
node.run(updatehash=updatehash)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
recon-all -all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-100206 -sd /output_dir/freesurfer -nomotioncor -notalairach -nonuintensitycor -nonormalization -noskullstrip -nogcareg -nocanorm -nocareg -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nosmooth2 -noinflate2 -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortribbon
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /output_dir/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rwxrwxrwx 1 503 dialout 416822 Mar 2 15:32 /output_dir/freesurfer/sub-100206/scripts/recon-all.log
Linux 065c02599775 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/output_dir/freesurfer/sub-100206/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Make White Surf lh Tue Mar 2 15:40:53 UTC 2021
/output_dir/freesurfer/sub-100206/scripts
mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs sub-100206 lh
#--------------------------------------------
#@# Make White Surf rh Tue Mar 2 15:40:53 UTC 2021
/output_dir/freesurfer/sub-100206/scripts
mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs sub-100206 rh
Waiting for PID 228 of (228 231) to complete...
Waiting for PID 231 of (228 231) to complete...
PIDs (228 231) completed and logs appended.
Linux 065c02599775 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-100206 exited with ERRORS at Tue Mar 2 15:40:57 UTC 2021
For more details, see the log file /output_dir/freesurfer/sub-100206/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingStandard error:
Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /opt/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/MiscUtilities.pm line 36.
BEGIN failed--compilation aborted at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/MiscUtilities.pm line 36.
Compilation failed in require at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/Spawn.pm line 35.
BEGIN failed--compilation aborted at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/Spawn.pm line 35.
Compilation failed in require at /opt/freesurfer/mni/bin/nu_correct line 38.
BEGIN failed--compilation aborted at /opt/freesurfer/mni/bin/nu_correct line 38.
Return code: 1
Traceback (most recent call last):
File "/opt/conda/envs/py37cmp-core/bin/connectomemapper3", line 159, in <module>
anat_pipeline.process()
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/cmp/pipelines/anatomical/anatomical.py", line 909, in process
anat_flow.run()
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
node.run(updatehash=updatehash)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/envs/py37cmp-core/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
recon-all -all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-100206 -sd /output_dir/freesurfer -nomotioncor -notalairach -nonuintensitycor -nonormalization -noskullstrip -nogcareg -nocanorm -nocareg -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nosmooth2 -noinflate2 -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortribbon
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /output_dir/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rwxrwxrwx 1 503 dialout 416822 Mar 2 15:32 /output_dir/freesurfer/sub-100206/scripts/recon-all.log
Linux 065c02599775 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/output_dir/freesurfer/sub-100206/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Make White Surf lh Tue Mar 2 15:40:53 UTC 2021
/output_dir/freesurfer/sub-100206/scripts
mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs sub-100206 lh
#--------------------------------------------
#@# Make White Surf rh Tue Mar 2 15:40:53 UTC 2021
/output_dir/freesurfer/sub-100206/scripts
mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs sub-100206 rh
Waiting for PID 228 of (228 231) to complete...
Waiting for PID 231 of (228 231) to complete...
PIDs (228 231) completed and logs appended.
Linux 065c02599775 4.19.76-linuxkit #1 SMP Thu Oct 17 19:31:58 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-100206 exited with ERRORS at Tue Mar 2 15:40:57 UTC 2021
For more details, see the log file /output_dir/freesurfer/sub-100206/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingStandard error:
Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname module) (@INC contains: /opt/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/MiscUtilities.pm line 36.
BEGIN failed--compilation aborted at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/MiscUtilities.pm line 36.
Compilation failed in require at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/Spawn.pm line 35.
BEGIN failed--compilation aborted at /opt/freesurfer/mni/lib/perl5/5.8.5/MNI/Spawn.pm line 35.
Compilation failed in require at /opt/freesurfer/mni/bin/nu_correct line 38.
BEGIN failed--compilation aborted at /opt/freesurfer/mni/bin/nu_correct line 38.
Return code: 1
... BIDS App execution command: ['docker', 'run', '-it', '--rm', '-v', '/Volumes/Drax/HCP/bids:/bids_dir', '-v', '/Volumes/Drax/HCP/bids/derivatives:/output_dir', '-v', '/Applications/freesurfer/license.txt:/bids_dir/code/license.txt', '-v', '/Volumes/Drax/HCP/bids/code/ref_anatomical_config.ini:/code/ref_anatomical_config.ini', '-u', '503:20', 'sebastientourbier/connectomemapper-bidsapp:v3.0.0-RC3', '/bids_dir', '/output_dir', 'participant', '--participant_label', '100206', '--anat_pipeline_config', '/code/ref_anatomical_config.ini', '--fs_license', '/bids_dir/code/license.txt', '--number_of_participants_processed_in_parallel', '1', '--number_of_threads', '1']
... $FS_LICENSE : /bids_dir/code/license.txt
* Number of subjects to be processed in parallel set to 1 (Total of cores available: 1)
Report execution to Google Analytics.
WARNING: rewriting config file /output_dir/cmp/sub-100206/sub-100206_anatomical_config.ini
... Anatomical config created : /output_dir/cmp/sub-100206/sub-100206_anatomical_config.ini
... Running pipelines :
... cmd : connectomemapper3 --bids_dir /bids_dir --output_dir /output_dir --participant_label sub-100206 --anat_pipeline_config /output_dir/cmp/sub-100206/sub-100206_anatomical_config.ini --number_of_threads 1