Usage

Execution and the BIDS format

The Multi-Scale Brain Parcellator workflow 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 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 Multi-Scale Brain Parcellator follow the BIDS-Apps definition with additional options specific to this pipeline.

Multi-scale Brain Parcellator BIDS App.

usage: multiscalebrainparcellator [-h]
                                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                                  [--number_of_cores NUMBER_OF_CORES]
                                  [--isotropic_resolution ISOTROPIC_RESOLUTION]
                                  [--thalamic_nuclei]
                                  [--hippocampal_subfields]
                                  [--brainstem_structures]
                                  [--skip_bids_validator] [-v]
                                  bids_dir output_dir {participant}

Positional Arguments

bids_dir	The directory with the input dataset formatted according to the BIDS standard.
output_dir	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 theparticipant level analysis.
analysis_level	Possible choices: participant Level of the analysis that will be performed. Note that only participant level analysis is available.Multiple participant level analyses can be run independently (in parallel) using the same output_dir.

Named Arguments

--participant_label
	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.
--number_of_cores
	The number of cores to be used forprocessing (Maximum number of available processing cores used by default)
--isotropic_resolution
	The isotropic resolution in mmused to resample the original anatomical imagesand applied a tthe beginning of the processing pipeline.
--thalamic_nuclei
	Whether or not to parcellate the thalamic nuclei Default: False
--hippocampal_subfields
	Whether or not to parcellate the hippocampal subfields Default: False
--brainstem_structures
	Whether or not to parcellate the brainstem structures Default: False
--skip_bids_validator
	Whether or not to perform BIDS dataset validation Default: False
-v, --version	Display the version of Multi-scale Brain Parcellator BIDS-App

Participant Level Analysis

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

docker run -it --rm \
-v /home/localadmin/data/ds001:/bids_dataset \
-v /media/localadmin/data/ds001/derivatives:/bids_dataset/derivatives \
-v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt \
sebastientourbier/multiscalebrainparcellator:latest \
/bids_dataset /bids_dataset/derivatives participant --participant_label 01 \
      --isotropic_resolution 1.0 \
      --thalamic_nuclei \
      --hippocampal_subfields \
      --brainstem_structures

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

Debugging

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

Support and communication

The documentation of this project is found here: http://multiscalebrainparcellator.readthedocs.org/en/latest/.

All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/sebastientourbier/multiscalebrainparcellator/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 multiscalebrainparcellator 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.