I have an issue that appear with 0.24 (my code was working with 0.23) with
Basically, for a sEEG analysis, I was importing my data in mri coord_frame, running my analysis and using
stc_near_sensor to prepare the plotting. All working well with 0.23.
montage = mne.channels.make_dig_montage(ch_pos, coord_frame='mri') raw.set_montage(montage) fig = mne.viz.plot_alignment(raw.info, trans=None, subject=subject, subjects_dir=subjects_dir, show_axes=True, surfaces=["pial"], coord_frame='mri') ... stc = mne.stc_near_sensors(evoked_plot, None, subject, src=vol_src, mode='nearest', subjects_dir=subjects_dir, distance=0.02)
With 0.24, I now get the following issue when using
RuntimeError: Channels must be in the head coordinate frame, got [0 (FIFFV_COORD_UNKNOWN)]
I believe it appeared because of this change introduced by @larsoner in this PR.
From what I could understand, it is a desired feature that all the coord_frames are in the head space.
To adapt to this change, I tried to add a transform as in the sEEG tutorial:
lpa, nasion, rpa = mne.coreg.get_mni_fiducials( patient, subjects_dir=subjects_dir) lpa, nasion, rpa = lpa['r'], nasion['r'], rpa['r'] montage = mne.channels.make_dig_montage(ch_pos, coord_frame='mri', nasion=nasion, lpa=lpa, rpa=rpa) trans = mne.channels.compute_native_head_t(montage) raw.set_montage(montage) fig = mne.viz.plot_alignment(raw.info, trans=trans, subject=subject, subjects_dir=subjects_dir, show_axes=True, surfaces=["pial"])
raw.info['chs']['coord_frame'] still gives me
0 (FIFFV_COORD_UNKNOWN), which will then results in an error in
So my questions:
- how to set the coordinate frame so that it is in the head space for sEEG data (somehow it works for the sEEG and ECoG tutorials, but I don’t quite get why (BTW, the sEEG electrodes are outside the brain in the sEEG tutorial, is this the desired output?))
- is it really not possible to leave it open to just use the mri coord_frame as before?
Thanks a lot for the help