This is a continuation of discussion from the following thread MarkupsLine .fcsv loads as MarkupsFiducials
@lassoan brought up the consideration of switching to
.json for handling Markup files in Slicer5. I think the simple answer from the perspective of the AFIDs project is that we will adapt to whatever specs are decided on for Slicer5, but ultimately we have interest in easily being able to convert between Slicer’s Markup file format and one that would be compatible with the Brain Imaging Data Structure (BIDS) specifications.
This may be a good time to try to determine if there is a point of convergence between the needs of both Slicer and BIDS for handling coordinates in
.json files that might eliminate the need for any conversion tool. However, this can get complicated if we are looking to decide on
.json fields that both Slicer and BIDS communities can agree on.
Compared with other aspects of the BIDS specification which are more mature, representation of coordinates remains a work in progress but is of interest to the community for different applications. The most recent version describing “Coordinate Systems” in the BIDS specification (v1.4.0) is here.
There have been different modality specific implementations (the one I’m most familiar with being iEEG) where the proposed solution is to use a paired set of files
.tsv to specify electrode locations: see https://www.nature.com/articles/s41597-019-0105-7#Sec4 and Figure 1e and 1f, which I’ve included. Having two files for Markups would likely be quite cumbersome in the Slicer environment.
I’d appreciate your thoughts and can loop in members of the BIDS community if interested. I also acknowledge that the Slicer user base likely has different needs than the BIDS/neuroimaging base, so having a converter tool as a go-between may be inevitable.