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ENH: Improve make_head_surface options #10592

Merged
merged 18 commits into from May 10, 2022
Merged

ENH: Improve make_head_surface options #10592

merged 18 commits into from May 10, 2022

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larsoner
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@larsoner larsoner commented May 3, 2022 •
edited

  1. Add threshold and mri to make_head_surface to allow using a different MRI (with a different threshold) using mkheadsurf.
  2. Add suggestion to smooth bad MRIs before calling make_head_surface.
  3. Add option fix_topology to allow fixing topology with pymeshfix.
  4. Move toward better/faster vtk imports using vtkmodules.
  5. Prefer head-dense.fif and head-sparse.fif when available (over -head.fif or outer_skin.surf) since these are more likely to be more accurate / better, as make_scalp_surfaces is more configurable than watershed_bem.

Todo:

larsoner added 12 commits May 3, 2022 16:01
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ENH: Improve make_head_surface options
d14f6bb
@larsoner
FIX: Import
5a67d56
@larsoner
FIX: Set
5a8511a
@larsoner
FIX: Order
1db66d1
@larsoner
FIX: Default
5442c83
@larsoner
FIX: For old FS
161ea9f
@larsoner
FIX: Revert
647f560
@larsoner
FIX: Validate
1e02c60
@larsoner
FIX: Req
75d135e
@larsoner
MAINT: Finish VTK imports
91303e3
@larsoner
Merge remote-tracking branch 'upstream/main' into make_head_surface
2318195 
* upstream/main:
  MRG: Add "highlight" parameter to Evoked.plot() to conveniently highlight time periods (mne-tools#10614)
  MRG: Allow to pass array of "average" values to plot_evoked_topomap() (mne-tools#10610)
  fix: snirf length units (mne-tools#10613)
  minor, doc: fix subplot titles in tutorial (mne-tools#10607)
  Display averaged time period in Evoked topomap title (mne-tools#10606)
  MAINT: Fix for pydata-sphinx-theme [skip azp][skip actions][circle deploy] (mne-tools#10605)
  DOC: report.add_html in tutorial (mne-tools#10603)
  Broader support of the SNIRF file format and enable reading GowerLab data (mne-tools#10555)
  MRG: Recommend mamba instead of libmamba for installation (mne-tools#10597)
  Fix dev documentation warning [skip azp][skip actions] (mne-tools#10599)
  FIX cmap (mne-tools#10593)
  [ENH, MRG] Add interpolate bridged electrodes function (mne-tools#10587)
@larsoner
TST: Add tests
ad59d8f
@larsoner larsoner marked this pull request as ready for review May 9, 2022 19:19
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larsoner commented May 9, 2022

Okay this is ready for review/merge from my end!

@larsoner larsoner mentioned this pull request May 9, 2022
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agramfort
agramfort approved these changes May 10, 2022
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note that pymeshfix is GPL licensed. Is this the first precedent in mne-python?

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note that pymeshfix is GPL licensed. Is this the first precedent in mne-python?

Argh I did not notice :( I've removed it and just noted it as a possible way to deal with bad meshes in a tutorial.

BTW my fix in the end for my bad lh.seghead ended up being to use the --mri param as suggested in the tutorial anyway, so it's perhaps not a huge loss to drop internal pymeshfix support!

@larsoner larsoner merged commit 754ea8e into mne-tools:main May 10, 2022
@larsoner larsoner deleted the make_head_surface branch May 10, 2022 18:26
larsoner added a commit to HanBnrd/mne-python that referenced this pull request May 17, 2022
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Merge remote-tracking branch 'upstream/main' into tddr-hb
bdfb2bb 
* upstream/main: (24 commits)
  Use less memory when loading EDF file (mne-tools#10638)
  BUG: fix ipython console accessibility after MNEQtBrowser in Spyder (mne-tools#10637)
  WIP: Fix mne.time_frequency.multitaper Nyquist adjustment slightly incorrect (mne-tools#10541)
  BUG: Fix bug with fNIRS reordering (mne-tools#10630)
  MNT: PyQt6 for pip pre 3.10 (mne-tools#10636)
  CI: Fix conda (mne-tools#10628)
  MRG: Update installer links to point to 1.0.3_0 (mne-tools#10622)
  [BUG, MRG] fix info write access (mne-tools#10626)
  [MRG] Fixed group_by titles in evoked_plot. (mne-tools#10618)
  [BUG, MRG] Replace image_interp with interpolation in topomap plot arguments (mne-tools#10617)
  MAINT: Fix timeout (mne-tools#10624)
  Simplify mne-tools#10619 (mne-tools#10620)
  Drop EEG rejection thresholds when replacing EEG with CSD channels (mne-tools#10619)
  Add get_montage support for fNIRS (mne-tools#10611)
  ENH: Improve make_head_surface options (mne-tools#10592)
  [ENH, MRG] Add citation for intracranial JOSS paper (mne-tools#10616)
  [ENH] Add sys info for mne-icalabel (mne-tools#10615)
  MRG: Add "highlight" parameter to Evoked.plot() to conveniently highlight time periods (mne-tools#10614)
  MRG: Allow to pass array of "average" values to plot_evoked_topomap() (mne-tools#10610)
  fix: snirf length units (mne-tools#10613)
  ...
@larsoner larsoner added the EOSS4 label Jun 7, 2022
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