Commandline Usage

Connectome Mapper 3 is distributed as a BIDS App which adopts the BIDS standard for data organization and takes as principal input the path of the dataset that is to be processed. The input dataset is required to be in valid BIDS format, and it must include at least a T1w or MPRAGE structural image and a DWI and/or resting-state fMRI image. See Connectome Mapper 3 and the BIDS standard page that provides links for more information about BIDS and BIDS-Apps as well as an example for dataset organization and naming.

Commandline Arguments

The command to run Connectome Mapper 3 follows the BIDS-Apps definition standard with additional options for loading pipeline configuration files.

Entrypoint script of the BIDS-App Connectome Mapper version v3.0.0-beta-RC2

usage: connectomemapper3 [-h]
                         [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                         [--session_label SESSION_LABEL [SESSION_LABEL ...]]
                         [--anat_pipeline_config ANAT_PIPELINE_CONFIG]
                         [--dwi_pipeline_config DWI_PIPELINE_CONFIG]
                         [--func_pipeline_config FUNC_PIPELINE_CONFIG]
                         [--number_of_participants_processed_in_parallel NUMBER_OF_PARTICIPANTS_PROCESSED_IN_PARALLEL]
                         [--fs_license FS_LICENSE] [-v]
                         bids_dir output_dir {participant,group}

Positional Arguments

bids_dir The directory with the input dataset formatted according to the BIDS standard.
output_dir The directory where the output files should be stored. If you are running group level analysis this folder should be prepopulated with the results of theparticipant level analysis.

Possible choices: participant, group

Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in parallel) using the same output_dir.

Named Arguments

 The label(s) of the participant(s) that should be analyzed. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include “sub-“). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list.
The label(s) of the
session that should be analyzed. The label corresponds to ses-<session_label> from the BIDS spec (so it does not include “ses-“). If this parameter is not provided all sessions should be analyzed. Multiple sessions can be specified with a space separated list.
 Configuration .txt file for processing stages of the anatomical MRI processing pipeline
 Configuration .txt file for processing stages of the diffusion MRI processing pipeline
 Configuration .txt file for processing stages of the fMRI processing pipeline
 The number of subjects to be processed in parallel (One core used by default).
--fs_license Freesurfer license.txt
-v, --version show program’s version number and exit


Before using any BIDS App, we highly recommend you to validate your BIDS structured dataset with the free, online BIDS Validator.

Participant Level Analysis

To run the docker image in participant level mode (for one participant):

$ docker run -t --rm -u $(id -u):$(id -g) \
        -v /home/localadmin/data/ds001:/bids_dir \
        -v /media/localadmin/data/ds001/derivatives:/output_dir \
        (-v /usr/local/freesurfer/license.txt:/bids_dir/code/license.txt \)
        sebastientourbier/connectomemapper3:v3.0.0-beta-RC2 \
        /bids_dir /output_dir participant --participant_label 01 \(--session_label 01 \)
            --anat_pipeline_config /bids_dir/code/ref_anatomical_config.ini \)
        (--dwi_pipeline_config /bids_dir/code/ref_diffusion_config.ini \)
        (--func_pipeline_config /bids_dir/code/ref_fMRI_config.ini \)
        (--number_of_participants_processed_in_parallel 1)


The local directory of the input BIDS dataset (here: /home/localadmin/data/ds001) and the output directory (here: /media/localadmin/data/ds001/derivatives) used to process have to be mapped to the folders /bids_dir and /output_dir respectively using the -v docker run option.


The user is requested to use its own Freesurfer license (available here). CMP expects by default to find a copy of the FreeSurfer license.txt in the code/ folder of the BIDS directory. However, one can also mount with the -v docker run option a freesurfer license.txt, which can be located anywhere on its computer (as in the example above, i.e. /usr/local/freesurfer/license.txt) to the code/ folder of the BIDS directory inside the docker container (i.e. /bids_dir/code/license.txt).


At least a configuration file describing the processing stages of the anatomical pipeline should be provided. Diffusion and/or Functional MRI pipeline are performed only if a configuration file is set. The generation of such configuration files, the execution of the BIDS App docker image and output inpection are facilitated through the use of the Connectome Mapper GUI, i.e. cmpbidsappmanager (see dedicated documentation page)


Logs are outputted into <output dir>/cmp/sub-<participant_label>/sub-<participant_label>_log-cmpbidsapp.txt.

Support, bugs and new feature requests

If you need any support or have any questions, you can post to the CMTK-users group.

All bugs, concerns and enhancement requests for this software are managed on GitHub and can be submitted at

Not running on a local machine? - Data transfer

If you intend to run connectomemapper3 on a remote system, you will need to make your data available within that system first. Comprehensive solutions such as Datalad will handle data transfers with the appropriate settings and commands. Datalad also performs version control over your data.