Input data requirements

The input dataset must be organised according to the BIDS data structure [GAC+16].

How RABIES traverses a dataset

RABIES iterates through every subject found to contain a functional file, and within each subject through the sessions and runs present.

When anatomical scans are used — that is, when --bold_only is not set — each functional scan is matched to one anatomical scan from the same subject and session.

Scan identification

Image type	Default BIDS suffixes	Parameter
Functional	bold, cbv	--bids_filter, key func
Structural	T1w, T2w	--bids_filter, key anat

Files matching neither filter are ignored. The default filter is equivalent to:

Listing 5 Default value of –bids_filter

{
    "func": {
        "suffix": ["bold", "cbv"]
    },
    "anat": {
        "suffix": ["T1w", "T2w"]
    }
}

See also

How to select which scans get processed for customising the filter and for selecting individual scans.

Image orientation

RABIES expects images in the NIfTI standard RAS+ orientation (Right–Anterior–Superior). Incorrectly oriented images are a common source of registration failures — see How to check image orientation.

Example dataset

The RABIES example dataset (test_dataset.zip) has the following structure:

Listing 6 Two subjects, one session each, with paired anatomical and functional scans

test_dataset/
├── sub-PHG001
│   └── ses-3
│       ├── anat
│       │   ├── sub-PHG001_ses-3_acq-RARE_T2w.json
│       │   └── sub-PHG001_ses-3_acq-RARE_T2w.nii.gz
│       └── func
│           ├── sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.json
│           └── sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz
└── sub-PHG002
    └── ses-3
        ├── anat
        │   ├── sub-PHG002_ses-3_acq-RARE_T2w.json
        │   └── sub-PHG002_ses-3_acq-RARE_T2w.nii.gz
        └── func
            ├── sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.json
            └── sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz

8 directories, 8 files

This is the dataset used in the tutorial.

Format conversion

Conversion from Bruker raw format to NIfTI can be handled with BrkRaw. The CoBrALab maintains notes on the conversion.