FIX make_watershed_bem to handle missing talairach_with_skull.lta courtesy Freesurfer 8#13172
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larsoner merged 12 commits intomne-tools:mainfrom Apr 3, 2025
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linux pip-pre error can be ignored (should be fixed by #13178), but the doc build error looks related: |
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looks reasonable to me, though I'm far from an expert with freesurfer.
Co-authored-by: Daniel McCloy <dan@mccloy.info>
larsoner
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* upstream/main: (149 commits) FIX make_watershed_bem to handle missing talairach_with_skull.lta courtesy Freesurfer 8 (mne-tools#13172) ENH: Add upsampling for MEG helmet surface (mne-tools#13179) MAINT: Update code credit (mne-tools#13180) BUG: Fix bug with least-squares sphere fit (mne-tools#13178) fix EDF export (mne-tools#13174) fix typo (mne-tools#13171) [pre-commit.ci] pre-commit autoupdate (mne-tools#13164) Fix dev installation guide (mne-tools#13163) expose 'mode' for plotting dipole on brain (mne-tools#13162) turn dipole attrs into properties (mne-tools#13153) remove misformatted (and unused) crossref anchor (mne-tools#13155) doc: point to read_dipole (mne-tools#13149) [pre-commit.ci] pre-commit autoupdate (mne-tools#13152) BUG: Fix bug with not short-circuiting n_jobs=1 (mne-tools#13147) FIX: Missing coordinates.xml in MFF file (mne-tools#13148) FIX: Gracefully handle bad XML files in EGI reader (mne-tools#13145) Fixes for Latest IPython (9.0.1) (mne-tools#13146) Fix intersphinx (mne-tools#13143) BUG: Fix bug with parallel doc build (mne-tools#13140) [pre-commit.ci] pre-commit autoupdate (mne-tools#13141) ...
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* upstream/main: (40 commits) fix typo (missing space) that messed up rst rendering (mne-tools#13217) MAINT: Restore VTK dev (mne-tools#13214) [pre-commit.ci] pre-commit autoupdate (mne-tools#13212) BUG: Fix bug with example (mne-tools#13210) MAINT: Fix pip-pre with PyVista (mne-tools#13207) Move FCBG to former partners (mne-tools#13205) ENH: Update related software list (mne-tools#13202) fix sfreq estimation for snirf files (mne-tools#13184) ENH: Use data-based padding instead of "odd" padding when filtering in raw.plot (mne-tools#13183) FIX: Bumps (mne-tools#13198) DOC: fix typo in examples/io/read_impedances.py (mne-tools#13197) [pre-commit.ci] pre-commit autoupdate (mne-tools#13173) FIX make_watershed_bem to handle missing talairach_with_skull.lta courtesy Freesurfer 8 (mne-tools#13172) ENH: Add upsampling for MEG helmet surface (mne-tools#13179) MAINT: Update code credit (mne-tools#13180) BUG: Fix bug with least-squares sphere fit (mne-tools#13178) fix EDF export (mne-tools#13174) fix typo (mne-tools#13171) [pre-commit.ci] pre-commit autoupdate (mne-tools#13164) Fix dev installation guide (mne-tools#13163) ...
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Fixes #13166.
Closes #13185.
What does this implement/fix?
Adds code to
bem.py/make_watershed_bemwith agcatlas=Truefor filesubject_dir + "/mri/transforms/talairach_with_skull.ltaand if the file doesn't exist (due to Freesurfer 8 not automatically generating it), runmri_em_register. Then proceed to run the regularmri_watershedcommand.Additional information
I debated doing a more comprehensive check of files before starting, but settled on a nested check with new cmd (
em_reg_cmd) and execution.There isn't currently a test for
mri_watershedintest_bem.pyand I don't currently have the time to add a comprehensive one.