Running mri_degad on your data

This section goes over the command line options you will find most useful when running mri_degad on your dataset, along with describing some issues you may face.

Note: Please first refer to the simple example in the Installation section, which goes over running mri_degad on a test dataset and the essential required options.

Including / excluding subjects to process

By default, mri_degad will run on all subjects in the dataset. If you wish to run on only a subset of subjects, you can use the --participant-label flag:

--participant-label 001

which would only run on sub-001. You can add additional subjects by passing a space-separated list to this option:

--participant-label 001 002

which would run for sub-001 and sub-002.

Similarly, subjects can be excluded from processing using the --exclude-participant-label flag.

BIDS Parsing limitations

mri_degad uses Snakebids, which makes use of pybids to parse a BIDS-compliant dataset. In mri_degad, a requirement is that all inputs processed need to have the acqusition (acq) entity with the value set to gad. mri_degad should have no problem parsing the following dataset:

PATH_TO_BIDS_DIR/
└── dataset_description.json
└── sub-001/
    └── anat/
        └── sub-001_acq-gad_T1w.nii.gz
└── sub-002/
    └── anat/
        ├── sub-002_acq-gad_T1w.nii.gz
...

as the path (with wildcards) will be interpreted as sub-{subject}_acq-{acq}_T1w.nii.gz.

However, because of the way Snakebids and Snakemake operate, one limitation is that the input files in your BIDS dataset needs to be consistent in terms of what optional BIDS entities exist in them. In the example below, one subject has a ses wildcard and one does not, resulting in an error from Snakebids.

PATH_TO_BIDS_DIR/
└── dataset_description.json
└── sub-001/
    └──ses-{ses}
        └── anat/
            ├── sub-001_ses-{ses}_acq-gad_T1w.nii.gz
└── sub-002/
    └── anat/
        ├── sub-002_acq-gad_T1w.nii.gz
...

because two distinct paths (with wildcards) would be found for T1w images: sub-{subject}_ses-{ses}_acq-gad_T1w.nii.gz and sub-{subject}_acq-gad_T1w.nii.gz.

There will soon be added functionality in Snakebids to filter out extra files, but for now, if your dataset has these issues, you will need to rename or remove extraneous files.