BIDS for spinal cord

[alexpron]

Dear BIDS experts,

I am working on BIDSifying a dataset that contains MRI images for both the brain and the spinal cord.

Currently the raw images of a subject/session are split into two subdirectories brain and spinalCord (e.g. sub-XXXX/brain) and the content in each of the two subdirectories respect BIDS standart. (e.g. anat/sub-XXXX_acq-c1c3_run-1_T2w.nii.gz). Ideally users of the dataset would like to keep the body part provenance in the filename so that it is easy to use to launch further processing (e.g. glob or parsing of a key)

I have found this example where I guess the part of the body scanned is not mentionned Data collection and organization — spine-generic documentation

An other example I have found is the courtois heudiconv heuristic where the body part is encoded as an entity (bp-) but this entity does not seems to be BIDS compliant (ds_prep/mri/convert/heuristics_unf.py at main · courtois-neuromod/ds_prep · GitHub)

I was wondering what was the best way to handle this case relying on BIDS standard.

Best,
Alexandre

[Steven]

Hi @alexpron,

@alexpron

Currently the raw images of a subject/session are split into two subdirectories brain and spinalCord (e.g. sub-XXXX/brain) and the content in each of the two subdirectories respect BIDS standart.

You’ll have to change that so everything is in one subject folder (that is, no brain subfolder).

@alexpron

Ideally users of the dataset would like to keep the body part provenance in the filename so that it is easy to use to launch further processing (e.g. glob or parsing of a key)

You can use something like acq-brain or acq-sc to differentiate the scans. Keep in mind that for apps such as fmriprep you should use a BIDS filter file to filter out spinal cord images. This should be easy to do if there is a consistent acq- labeling scheme as suggested above.

Best,
Steven