Connectome Mapper 3 is distributed as a BIDS App which adopts the BIDS (Brain Imaging Data Structure) 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 cmpbids page that provides links for more information about BIDS and BIDS-Apps as well as an example for dataset organization and naming.
The command to run Connectome Mapper 3 follows the BIDS-Apps definition standard with additional options for loading pipeline configuration files.
Important
Before using any BIDS App, we highly recommend you to validate your BIDS structured dataset with the free, online BIDS Validator.
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: \ /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)
Note
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.
Important
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).
Note
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.
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 https://github.com/connectomicslab/connectomemapper3/issues.
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.