Thanks for the info. Although it's not exactly the same approach, the idea to save the head-points-aligned coregistration in the BIDS metadata is. I looked at the link you provided, and the MNE coregsitration tutorial
. If you don't mind, can you confirm if I understood correctly?
During coregistration in MNE, you can manually mark anatomical landmarks on the head surface, but if you later use the head points to improve the coregistration, these marked points are no longer used at all. Instead, it's the digitized landmarks that define the "head" coordinate frame. (Note that in Brainstorm it's the opposite: the digitized landmarks are ignored after aligning with the head points and the ones picked on the MRI define the subject coordinate space.)
Thus to save the coregistration info in BIDS, you bring the digitized landmarks into MRI voxel coordinates and save those in the t1w.json file. This means that for multiple MEG sessions, you could in theory have multiple sets of landmarks saved in this t1w.json file, correct? (This is the part I don't like as much.)
In comparison, my suggestion 1 keeps one set of manually marked MRI landmarks in the t1w.json file, and following the Brainstorm convention, bring these into the head space to be saved along each MEG session in a _coordsystem.json file. The disadvantage here is that these coordinates no longer match the digitized landmarks.
I think both approaches are "BIDS valid" and make sense following the MNE or Brainstorm conventions. However, both have inconveniences in terms of software:
- "MNE": non-standard naming of landmarks from multiple MEG sessions in t1w.json.
- "Brainstorm": prefer the _coordsystem.json landmarks over the digitized ones.
And in both cases, it may not be clear whether the BIDS landmarks already include the head points fit.
Any further comments?