Skip to content

Latest commit

 

History

History
101 lines (68 loc) · 4.01 KB

usage.rst

File metadata and controls

101 lines (68 loc) · 4.01 KB
Raw

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 (Brain Imaging Data Structure) format, and it must include at least one T1w or MPRAGE structural image. For example:

ds-example/

    README
    CHANGES
    participants.tsv
    dataset_description.json

    sub-01/
        anat/
            sub-01_T1w.nii.gz
            sub-01_T1w.json

    ...

    sub-<subject_label>/
        anat/
            sub-<subject_label>_T1w.nii.gz
            sub-<subject_label>_T1w.json
        ...
    ...

For more information about BIDS, please consult the BIDS Website and the Online BIDS Specifications. HeuDiConv can assist you in converting DICOM brain imaging data to BIDS. A nice tutorial can be found @ BIDS Tutorial Series: HeuDiConv Walkthrough .

Important

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.

More information about BIDS Apps? Please check directly on the BIDS Apps Website.

Participant Level Analysis

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

$ docker run -it --rm \
-v /home/localadmin/data/ds-example:/bids_dir \
-v /media/localadmin/data/ds-example/derivatives:/output_dir \
-v /usr/local/freesurfer/license.txt:/bids_dir/code/license.txt \
sebastientourbier/multiscalebrainparcellator:v1.1.0 \
/bids_dir /output_dir participant --participant_label 01 \
--isotropic_resolution 1.0 \
--thalamic_nuclei \
--hippocampal_subfields \
--brainstem_structures

Important

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

Multi-scale brain parcellator needs your own Freesurfer license. As a result, you must map your license (for instance /usr/local/freesurfer/license.txt) to the file /bids_dir/code/license.txt inside the BIDS App.

Debugging

Logs are outputted to sub-<participant_label>_log-multiscalebrainparcellator.txt located in <output dir>/cmp/sub-<participant_label>/ directory.

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.