To run the script in participant level mode (for processing one subject only), use e.g.:
$ docker run -i --rm \
-v /Users/yourname/data:/bids_dataset \
-v /Users/yourname/outputs:/outputs \
bids/mrtrix3_connectome \
/bids_dataset /outputs participant --participant_label 01 --parcellation desikan
Following processing of all participants, the script can be run in group analysis mode using e.g.:
$ docker run -i --rm \
-v /Users/yourname/data:/bids_dataset \
-v /Users/yourname/output:/output \
bids/mrtrix3_connectome \
/bids_dataset /output group
https://github.com/BIDS-Apps/MRtrix3_connectome
To run the script in participant level mode (for processing one subject only), use e.g.:
$ docker run -i --rm \ -v /Users/yourname/data:/bids_dataset \ -v /Users/yourname/outputs:/outputs \ bids/mrtrix3_connectome \ /bids_dataset /outputs participant --participant_label 01 --parcellation desikan Following processing of all participants, the script can be run in group analysis mode using e.g.:
$ docker run -i --rm \ -v /Users/yourname/data:/bids_dataset \ -v /Users/yourname/output:/output \ bids/mrtrix3_connectome \ /bids_dataset /output group