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ENH: agenda for beamformer module

See original GitHub issue

Let’s keep record of what issues and enhancements are still open with the beamformer code (not including visualization etc.). Here is a list of open issues and PRs and other things that need to be done:

  • Eigenvalue inversion beamformer (“automatic” regularization) This is in issues #5362 and #5690.
  • Clarify SAM vs LCMV in docstring of LCMV
  • Non-converging test results with reg=0.0 Check out why one of the beamformer tests in test_lcmv does not converge across CIs for reg=0. For discussion and link to specific test, see https://github.com/mne-tools/mne-python/pull/6042#discussion_r265037976
  • Address combination of different sensor types in DICS The combination of different sensor types when computing the CSD matrix needs to be addressed, for discussion see #5135, #7021
  • Center of head bias even with normalization #5266
  • Pass covariance to beamformer to get static image This is issue #5229. It relates _lcmv_source_power, which could need some work / refactoring with make_lcmv.
  • Speed up LCMV Speed up the LCMV code and the LCMV tests. (This was taken care of in some PR already. Also in #6603)
  • Have beamformers use mne.minimum_norm._prepare_forward #5881 (#6042)
  • Port MNE depth bias tests to LCMV #5984
  • Projections in beamfomer code Still open from #5135: how should DICS handle projections? (Also related to #5342 - is LCMV handling projections the right way?)
  • [BUG] Orienation selection in unit-noise-gain DICS Compare this comment, the normalization done at the beginning of the DICS pipeline results in a wrong orientation selection formula
  • Further refactoring of the DICS/LCMV code Once the DICS bug (see above) is solved, the last steps of refactoring can be done (confirm equal results when switching DICS and LCMV computation blocks), this concerns this code block (review). At the moment, results do not converge, probably due to the DICS orientation selection bug.
  • Orienation selection for unit-gain LCMV This is started in #4659 and is waiting for easy access to leadfield normalization, which should be granted after merging the refactoring PR #5135.
  • Store orientations in filters object Store the picked source orientation in the spatial filter, e.g., for plotting.
  • NAI for DICS beamformer as suggested by @mmagnuski in #5135

And then, there is this older issue about beamformer enhancements: #3853. Some of this is done now, but other things might remain, like the different output types (z-scores etc. - which, however, could also just be computed on the output directly).

Anything missing, @agramfort @larsoner @sarangnemo @wmvanvliet ?

Issue Analytics

  • State:open
  • Created 5 years ago
  • Reactions:2
  • Comments:16 (16 by maintainers)

github_iconTop GitHub Comments

1reaction
mmagnuskicommented, Dec 17, 2018

(I just moved unchecked checkboxes to the top to make them more visible)

0reactions
britta-wstnrcommented, Sep 12, 2019

@larsoner I don’t think any of the things here are critical. @wmvanvliet and I have some work planned in October (relating to the Spring Coding Sprint comparison between types) and hopefully will close the pending issues along the way!

Read more comments on GitHub >

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