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
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/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
Support and communication
The documentation of this project is found here: https://connectome-mapper-3.readthedocs.io/en/latest/.
All bugs, concerns and enhancement requests for this software can be submitted here: https://gitlab.com/connectomicslab/connectomemapper3/issues.
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.