I’ve been trying to use Connectome Mapper 3 but am having troubles with executing the command.
I generated the configuration files as described here.
My BIDS data set is validated.
I’m trying to execute the command via docker:
docker run -t --rm \
-v /media/groot/Data/BeforeAfterCovid19_BIDS_dataset:/bids_dir \
-v /media/groot/Data/BeforeAfterCovid19_derivatives/cmp_derivatives:/output_dir \
sebastientourbier/connectomemapper-bidsapp:v3.0.0-RC1 /bids_dir /output_dir participant --participant_label 0010 --fs_license /bids_dir/code/license.txt --anat_pipeline_config /bids_dir/code/ref_anatomical_config.ini --dwi_pipeline_config /bids_dir/code/ref_diffusion_config.ini
(I’m only trying to analyze subject 0010 data to see the way these pipelines work)
I receive the following error:
User: root
Group: root
> BIDS dataset: /bids_dir
> Subjects to analyze : ['0010']
> Set $FS_LICENSE which points to FreeSurfer license location (BIDS App)
... $FS_LICENSE : /bids_dir/code/license.txt
* Number of subjects to be processed in parallel set to one (sequential run)
* Number of parallel threads set to one (total of cores: 23)
* OMP_NUM_THREADS set to 1 (total of cores: 23)
> Sessions to analyze : ['ses-1', 'ses-2']
> Process subject sub-0010 session ses-1
WARNING: rewriting config file /output_dir/cmp/sub-0010/ses-1/sub-0010_ses-1_anatomical_config.ini
... Anatomical config created : /output_dir/cmp/sub-0010/ses-1/sub-0010_ses-1_anatomical_config.ini
WARNING: rewriting config file /output_dir/cmp/sub-0010/ses-1/sub-0010_ses-1_diffusion_config.ini
... Diffusion config created : /output_dir/cmp/sub-0010/ses-1/sub-0010_ses-1_diffusion_config.ini
... Running pipelines :
- Anatomical MRI (segmentation and parcellation)
- Diffusion MRI (structural connectivity matrices)
INFO: functional pipeline not performed
Traceback (most recent call last):
File "/app/connectomemapper3/run.py", line 497, in <module>
number_of_threads=number_of_threads)
File "/app/connectomemapper3/run.py", line 73, in create_cmp_command
return ' '.join(cmd)
TypeError: sequence item 14: expected str instance, int found
Anyone knows how to fix this issue?
Thank you,
Gal.