BIDS and BIDS App standards

MIALSRTK BIDS App adopts the BIDS standard for data organization and is developed following the BIDS App standard. This means that MIALSRTK BIDS App handles dataset formatted following the BIDS App standard and provides a processing workflow containerized in Docker container image (promoting portability and reproduciblity) that can be run with a set of arguments defined by the BIDS App standard directly from the terminal or a script (See Commandline Usage section for more details).

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

BIDS dataset schema

The BIDS App accepts BIDS datasets that adopt the following organization, naming, and file formats:

ds-example/

    README
    CHANGES
    participants.tsv
    dataset_description.json

    sub-01/
        anat/
            sub-01_run-1_T2w.nii.gz
            sub-01_run-1_T2w.json
            sub-01_run-2_T2w.nii.gz
            sub-01_run-2_T2w.json
            ...

    ...

    sub-<subject_label>/
        anat/
            sub-<subject_label>_run-1_T2w.nii.gz
            sub-<subject_label>_run-1_T2w.json
            sub-<subject_label>_run-2_T2w.nii.gz
            sub-<subject_label>_run-2_T2w.json
            ...
        ...
    ...

    code/
        participants_params.json

where participants_params.json is the MIALSRTK BIDS App configuration file, which follows a specific schema (See config schema), and which defines multiple processing parameters (such as the ordered list of scans or the weight of regularization).

Important

Before using any BIDS App, we highly recommend you to validate your BIDS structured dataset with the free, online BIDS Validator.