our lab has been working on a collection of cerebellar atlases for a while now. For the next release, I decided to bring the atlas collection into a BIDS-like standard, loosely based on templateflow.
The collection is on github as a git/datalad repository:
I’m looking for input / feedback on:
a) Is there a more developed BIDS-standard on volume / surface based brain atlases (label and contrast maps) that I should look into?
b) Is the current structure helpful - do you have suggestions for changes or additions?
c) For the label-atlases, are *.lut or *.tsv files more helpful?
d) Any cerebellar maps / data that is missing - or that you want to contribute?
Once we have a stable version, I am also planning to integrate it with our online Atlas viewer.
online atlas viewer
I have faced the same problem recently when trying to organize ROI images (either at the group level or the subject level).
My suggestion would be to try to get as much mileage as possible from the BIDS derivatives specification for segmentation (that covers both surface and volume data)
specification: Imaging data types - Brain Imaging Data Structure v1.6.0
starter kit: The BIDS folder hierarchy · bids-standard/bids-starter-kit Wiki · GitHub
- so use a tsv file and not LUT
- as much as possible try to stick to the entities that already exist in BIDS (with the set of entities for derivatives you should be able to cover a lot of use cases)
- if that’s not possible and you need more flexibility in your filenames try to stick to the format
<entity-name>*_suffix.extension to be as BIDSy as possible
hope that helps
Thanks - didn’t see that Data Structure page before - that’s very helpful.
For ease of use, it maybe good to provide a quick function to translate tsv files to LUT, and / or the FSL atlas XML files? Or somewhere in the BIDS world there should already be a package / function for this?
Just saw your response now.
That’s a good point. I am not aware of anything like this as part of pybids and it is not in bids-matlab.
If they are small enough they could go as standalone functions on the bids starter kit.
Only realize now that I forgot to mention that both pybids and bids-matlab can help you create bids compatible name files if you need to script that somehow.