BIDS

What is a BIDS way to name and store Regions of Interest (ROIs)?

There is no “official” way to name ROI in BIDS, but you can apply BIDS naming principles to name those.

The closest things to ROI naming are the masks for the BIDS derivatives.

Here is an example from the :ref:face repetition demo::

  bidspm-roi
  ├── group
  │   ├── hemi-L_space-MNI_label-V1d_desc-wang_mask.json
  │   ├── hemi-L_space-MNI_label-V1d_desc-wang_mask.nii
  │   ├── hemi-L_space-MNI_label-V1v_desc-wang_mask.json
  │   ├── hemi-L_space-MNI_label-V1v_desc-wang_mask.nii
  │   ├── hemi-R_space-MNI_label-V1d_desc-wang_mask.json
  │   ├── hemi-R_space-MNI_label-V1d_desc-wang_mask.nii
  │   ├── hemi-R_space-MNI_label-V1v_desc-wang_mask.json
  │   └── hemi-R_space-MNI_label-V1v_desc-wang_mask.nii
  └── sub-01
      └── roi
          ├── sub-01_hemi-L_space-individual_label-V1d_desc-wang_mask.nii
          ├── sub-01_hemi-L_space-individual_label-V1v_desc-wang_mask.nii
          ├── sub-01_hemi-R_space-individual_label-V1d_desc-wang_mask.nii
          └── sub-01_hemi-R_space-individual_label-V1v_desc-wang_mask.nii

ROIs that are defined in some MNI space are going to be the same across subjects, so you could store a “group” folder (this is not BIDSy but is less redundant than having a copy of the same file for each subject).

The desc entity (description) here is used to denotate the atlas the ROI taken from, so if you are building yours from a localizer you might not need to use it.

Ideally you would want to add a JSON file to add metadata about those ROIs.

You can use bids-matlab to help you create BIDS valid filenames.

  >> name_spec.ext = '.nii';
  >> name_spec.suffix = 'mask';
  >> name_spec.entities = struct( ...
                                'hemi', 'R', ...
                                'space', 'MNI', ...
                                'label', 'V1v', ...
                                'desc', 'wang');
  >> file = bids.File(name_spec);
  >> file.filename

     hemi-R_space-MNI_label-V1v_desc-wang_mask.nii

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