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Commandline Usage


The Connectome Mapper 3 BIDS App takes as principal input the path of the dataset that is to be processed. The input dataset is required to be in valid :abbr:`BIDS (Brain Imaging Data Structure)` format, and it must include at least one T1w or MPRAGE structural image. We highly recommend that you validate your dataset with the free, online BIDS Validator.

Commandline Arguments

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

.. argparse::
                :ref: cmp.parser.get
                :prog: connectomemapper3

Participant Level Analysis

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

docker run -it --rm \
        -v /home/localadmin/data/ds001:/tmp \
        -v /media/localadmin/data/ds001/derivatives:/tmp/derivatives \
        -v /usr/local/freesurfer/license.txt:/tmp/code/license.txt \
        sebastientourbier/connectomemapper3:latest \
        /tmp /tmp/derivatives participant --participant_label 01 \
            --anat_pipeline_config /tmp/code/ref_anatomical_config.ini \
        (--dwi_pipeline_config /tmp/code/ref_diffusion_config.ini \)
        (--func_pipeline_config /tmp/code/ref_fMRI_config.ini \)


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 /tmp and /tmp/derivatives respectively using the -v docker run option.


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.


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

Support and communication

The documentation of this project is found here:

All bugs, concerns and enhancement requests for this software can be submitted here:

If you run into any problems or have any questions, you can post to the CMTK-users group.

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.

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