Commandline Usage

Connectome Mapper 3 (CMP3) 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 and/or preprocessed EEG data. 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.


As of CMP3 v3.0.0-RC2, the BIDS App includes a tracking system that anonymously reports the run of the BIDS App. This feature has been introduced to support us in the task of fund finding for the development of CMP3 in the future. However, users are still free to opt-out using the --notrack commandline argument.


Since v3.0.0-RC4, configuration files adopt the JSON format. If you have your configuration files still in the old INI format, do not worry, the CMP3 BIDS App will convert them to the new JSON format automatically for you.

Commandline Arguments

The command to run CMP3 follows the BIDS-Apps definition standard with additional options for loading pipeline configuration files.

Entrypoint script of the BIDS-App Connectome Mapper version v3.2.0

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]
                         [--eeg_pipeline_config EEG_PIPELINE_CONFIG]
                         [--number_of_threads NUMBER_OF_THREADS]
                         [--number_of_participants_processed_in_parallel NUMBER_OF_PARTICIPANTS_PROCESSED_IN_PARALLEL]
                         [--mrtrix_random_seed MRTRIX_RANDOM_SEED]
                         [--ants_random_seed ANTS_RANDOM_SEED]
                         [--ants_number_of_threads ANTS_NUMBER_OF_THREADS]
                         [--fs_license FS_LICENSE] [--coverage] [--notrack]
                         bids_dir output_dir {participant,group}

Positional Arguments


The directory with the input dataset formatted according to the BIDS standard.


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 the participant 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 .json file for processing stages of the anatomical MRI processing pipeline


Configuration .json file for processing stages of the diffusion MRI processing pipeline


Configuration .json file for processing stages of the fMRI processing pipeline


Configuration .json file for processing stages of the eeg processing pipeline


The number of OpenMP threads used for multi-threading by Freesurfer (Set to [Number of available CPUs -1] by default).


The number of subjects to be processed in parallel (One by default).

Default: 1


Fix MRtrix3 random number generator seed to the specified value


Fix ANTS random number generator seed to the specified value


Fix number of threads in ANTs. If not specified ANTs will use the same number as the number of OpenMP threads (see —-number_of_threads option flag)


Freesurfer license.txt


Run connectomemapper3 with coverage

Default: False


Do not send event to Google analytics to report BIDS App execution, which is enabled by default.

Default: False

-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

You can run CMP3 using the lightweight Docker or Singularity wrappers we created for convenience or you can interact directly with the Docker / Singularity Engine via the docker or singularity run command.

New in v3.0.2 ✨

You can now be aware about the adverse impact of your processing on the environment 🌍🌳!

With the new –track_carbon_footprint option of the connectomemapper3_docker and connectomemapper3_singularity BIDS App python wrappers, you can use codecarbon to estimate the amount of carbon dioxide (CO2) produced to execute the code by the computing resources and save the results in <bids_dir>/code/emissions.csv.

Then, to visualize, interpret and track the evolution of the CO2 emissions incurred, you can use the visualization tool of codecarbon aka carbonboard that takes as input the .csv created:

$ carbonboard --filepath="<bids_dir>/code/emissions.csv" --port=xxxx

With the wrappers

When you run connectomemapper3_docker, it will generate a Docker command line for you, print it out for reporting purposes, and then execute it without further action needed, e.g.:

$ connectomemapper_docker \
     "/home/user/data/ds001" "/home/user/data/ds001/derivatives" \
     participant --participant_label 01 --session_label 01 \
     --fs_license "/usr/local/freesurfer/license.txt" \
     --config_dir "/home/user/data/ds001/code" \
     --track_carbon_footprint \
     --anat_pipeline_config "ref_anatomical_config.json" \
     (--dwi_pipeline_config "ref_diffusion_config.json" \)
     (--func_pipeline_config "ref_fMRI_config.json" \)
     (--eeg_pipeline_config "ref_EEG_config.json" \)
     (--number_of_participants_processed_in_parallel 1)

When you run connectomemapper3_singularity, it will generate a Singularity command line for you, print it out for reporting purposes, and then execute it without further action needed, e.g.:

$ connectomemapper3_singularity \
     "/home/user/data/ds001" "/home/user/data/ds001/derivatives" \
     participant --participant_label 01 --session_label 01 \
     --fs_license "/usr/local/freesurfer/license.txt" \
     --config_dir "/home/user/data/ds001/code" \
     --track_carbon_footprint \
     --anat_pipeline_config "ref_anatomical_config.json" \
     (--dwi_pipeline_config "ref_diffusion_config.json" \)
     (--func_pipeline_config "ref_fMRI_config.json" \)
     (--eeg_pipeline_config "ref_EEG_config.json" \)
     (--number_of_participants_processed_in_parallel 1)

With the Docker / Singularity Engine

If you need a finer control over the container execution, or you feel comfortable with the Docker or Singularity Engine, avoiding the extra software layer of the wrapper might be a good decision.


For instance, the previous call to the connectomemapper3_docker wrapper corresponds to:

$ docker run -t --rm -u $(id -u):$(id -g) \
        -v /home/user/data/ds001:/bids_dir \
        -v /home/user/data/ds001/derivatives:/output_dir \
        (-v /usr/local/freesurfer/license.txt:/bids_dir/code/license.txt) \
        sebastientourbier/connectomemapper-bidsapp:v3.2.0 \
        /bids_dir /output_dir participant --participant_label 01 (--session_label 01) \
        --anat_pipeline_config /bids_dir/code/ref_anatomical_config.json \
        (--dwi_pipeline_config /bids_dir/code/ref_diffusion_config.json \)
        (--func_pipeline_config /bids_dir/code/ref_fMRI_config.json \)
        (--eeg_pipeline_config /bids_dir/code/ref_EEG_config.json \)
        (--number_of_participants_processed_in_parallel 1)


For instance, the previous call to the connectomemapper3_singularity wrapper corresponds to:

$ singularity run  --containall \
        --bind /home/user/data/ds001:/bids_dir \
        --bind /home/user/data/ds001/derivatives:/output_dir \
        --bind /usr/local/freesurfer/license.txt:/bids_dir/code/license.txt \
        library://connectomicslab/default/connectomemapper-bidsapp:v3.2.0 \
        /bids_dir /output_dir participant --participant_label 01 (--session_label 01) \
        --anat_pipeline_config /bids_dir/code/ref_anatomical_config.json \
        (--dwi_pipeline_config /bids_dir/code/ref_diffusion_config.json \)
        (--func_pipeline_config /bids_dir/code/ref_fMRI_config.json \)
        (--eeg_pipeline_config /bids_dir/code/ref_EEG_config.json \)
        (--number_of_participants_processed_in_parallel 1)


The local directory of the input BIDS dataset (here: /home/user/data/ds001) and the output directory (here: /home/user/data/ds001/derivatives) used to process have to be mapped to the folders /bids_dir and /output_dir respectively using the docker -v / singularity --bind 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 a freesurfer license.txt with the docker -v / singularity --bind run option. This file can be located anywhere on the 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 saved into <output dir>/cmp/sub-<participant_label>/sub-<participant_label>_log.txt.

Already have Freesurfer outputs?

If you have already Freesurfer v5 / v6 output data available, CMP3 can use them if there are properly placed in your output / derivatives directory. Since v3.0.3, CMP3 expects to find a freesurfer-7.1.1, so make sure that your derivatives are organized as follows:

  |______ derivatives/
  |         |______ freesurfer-7.1.1/
  |                   |______ sub-01[_ses-01]/
  |                   |           |______ label/
  |                   |           |______ mri/
  |                   |           |______ surf/
  |                   |           |______ ...
  |                   |______ ...
  |______ sub-01/
  |______ ...

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?

If you intend to run CMP3 on a remote system such as a high-performance computing cluster where Docker is not available due to root privileges, a Singularity image is also built for your convenience and available on Please see instructions at Running on a cluster (HPC).

Also, 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. A tutorial is provided in Adopting Datalad for collaboration.