Revert "Add error message when conversion of EEG locs to head space f… #11104
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…ails (mne-tools#11080)" This reverts commit bdc435d.
agramfort
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Aug 28, 2022
larsoner
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Aug 28, 2022
| d['r'] = apply_trans(native_head_t, d['r']) | ||
| d['coord_frame'] = FIFF.FIFFV_COORD_HEAD | ||
| elif d['kind'] == FIFF.FIFFV_POINT_EEG: | ||
| raise RuntimeError( |
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Instead of reverting, can/should we now consider a _on_missing style behavior, perhaps with a default of on_frame_mismatch='warn' (and what you had here would have been equivalent to on_mismatch='raise')? MNE-BIDS could inspect the _get_args and see if 'on_frame_mismatch' is in there, and add on_frame_mismatch='ignore'
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I'd rather fix MNE-BIDS and then bring back the error ;)
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Thanks @wmvanvliet ! I reopened #10946 so we don't forget to fix it somehow in MNE-BIDS |
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* upstream/main: Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104) MRG: Fixes for mne-tools#11090 (mne-tools#11108) add test for edf units param (mne-tools#11105) BUG: Improve logic for bti (mne-tools#11102) add spectrum class (mne-tools#10184) ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099) ENH: Add temperature and galvanic (mne-tools#11090)
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* upstream/main: (366 commits) BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115) Add API entry list and map (mne-tools#10999) Add legacy decorator (mne-tools#11097) [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095) Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104) MRG: Fixes for mne-tools#11090 (mne-tools#11108) add test for edf units param (mne-tools#11105) BUG: Improve logic for bti (mne-tools#11102) add spectrum class (mne-tools#10184) ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099) ENH: Add temperature and galvanic (mne-tools#11090) Add error message when conversion of EEG locs to head space fails (mne-tools#11080) DOC: removed unnecessary line in PSF example (mne-tools#11085) FIX: Update helmet during ICP (mne-tools#11084) Fix various typos (mne-tools#11086) DOC: Rel BUG: don't assume that channel info contains particular keys (mne-tools#11074) [BUG] Fix plot_topomap with sphere="eeglab" (mne-tools#11081) Add `vmin` and `vmax` specification to `mne.Evoked.animate_topomap` (mne-tools#11073) Add _on_missing functionality to UpdateChannelsMixin (mne-tools#11077) ...
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* upstream/main: (25 commits) DOC: Exclude some implicit refs in doc build (mne-tools#10433) MAINT: Better issue forms (mne-tools#11101) [FIX] Typo in example (mne-tools#11118) [MRG] Improve interpolation of bridged electrodes (mne-tools#11094) BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115) Add API entry list and map (mne-tools#10999) Add legacy decorator (mne-tools#11097) [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095) Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104) MRG: Fixes for mne-tools#11090 (mne-tools#11108) add test for edf units param (mne-tools#11105) BUG: Improve logic for bti (mne-tools#11102) add spectrum class (mne-tools#10184) ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099) ENH: Add temperature and galvanic (mne-tools#11090) Add error message when conversion of EEG locs to head space fails (mne-tools#11080) DOC: removed unnecessary line in PSF example (mne-tools#11085) FIX: Update helmet during ICP (mne-tools#11084) Fix various typos (mne-tools#11086) DOC: Rel ...
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This reverts commit bdc435d.
Turns out that MNE-BIDS abuses
set_montagea bit when reading montages. For example, intutorials/clinical/30_ecog.py,read_raw_bidsreturns the channel positions as a montage applied to theRaw, in MRI coordinates, violating our convention. Then, the montage is fixed manually in the tutorial by callingraw.get_montage, transforming to head coordinates, and then callingraw.set_montageagain.Ideally, MNE-BIDS should have a separate
read_montage_bidsfunction, so it wouldn't have to rely on montages being applied to a raw object.fixes #11100