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[ENH] Add support for the BIDS template coordinate frames

See original GitHub issue

Related to https://github.com/mne-tools/mne-bids/issues/961 and https://github.com/mne-tools/mne-bids/pull/962.

Both EEG and iEEG data can be stored in any of the template coordinate frames in BIDS https://bids-specification.readthedocs.io/en/stable/99-appendices/08-coordinate-systems.html#eeg-specific-coordinate-systems. If one of these coordinate frames is used, MNE-Python could have an internal representation for it in transforms.py. The question is what would we need? What comes to mind are 1) a mapping in FIF for roundtrip save/load, 2) the fiducials in this coordinate frame to transform it to other coordinate frames and 3) optionally, the template MR image itself for examples (and potentially also the freesurfer recon but that’s going to be quite a bit of data).

Once this is done, a montage object could have apply_trans used and be in that coordinate frame to save to BIDS using mne_bids.write_raw_bids and then could also be read out using mne_bids.read_raw_bids and it would have an official named integer representation and work just like the other coordinate frames.

I think the hardest part would be figuring out the representation in the FIF standard. Do you know if this would be easy or very hard @larsoner or @agramfort?

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:18 (18 by maintainers)

github_iconTop GitHub Comments

1reaction
larsonercommented, Mar 1, 2022

Hopefully you can convince others that this limited support for coordinate frames is ultimately a good thing and not laziness on our part 😃

0reactions
alexrockhillcommented, Mar 1, 2022

Okay, good discussion, let’s have it all be MNE-BIDS-level tutorial, I agree.

Read more comments on GitHub >

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