Description of the problem
Trying to use stc_near_sensors there is one bug if there are any bad channels, that causes
if picks is None:
picks = pick_types(evoked.info, ecog=True, seeg=True, dbs=True)
evoked = evoked.copy().pick(picks)
frames = set(evoked.info["chs"][pick]["coord_frame"] for pick in picks)
This to fail with an index error because when evoked gets picked the bad channels aren't included.
There is another bug/API confusion that the default for surface is 'pial' so if you pass a volume source estimate and no argument for surface then you get an index error because it tried to use the pial surface which has the wrong indices for your volume source estimate. That seems unnecessarily confusing, I think it should work reasonably with default arguments for both surface and volume source estimates.
Also while doing a MWE, this link in the issue template is broken https://mne.tools/dev/overview/datasets_index.html.
Steps to reproduce
import mne
misc_path = mne.datasets.misc.data_path()
subjects_dir = misc_path / "seeg"
raw = mne.io.read_raw(misc_path / "seeg" / "sample_seeg_ieeg.fif")
raw.info['bads'] = ['LENT 1']
trans = mne.coreg.estimate_head_mri_t("sample_seeg", subjects_dir)
epochs = mne.Epochs(raw, detrend=1, baseline=None)
epochs = epochs["Response"][0] # just process one epoch of data for speed
evoked = epochs.average()
surface = subjects_dir / "sample_seeg" / 'bem' / 'inner_skull.surf'
vol_src = mne.setup_volume_source_space(
subject="sample_seeg", subjects_dir=subjects_dir, surface=surface,
pos=10)
vol_stc = mne.stc_near_sensors(
evoked, trans, subject="sample_seeg",
subjects_dir=subjects_dir, src=vol_src) # surface=None)Link to data
No response
Expected results
Working stc
Actual results
Two index errors
File ~/projects/mne-python/mne/source_estimate.py:3878, in <genexpr>(.0)
3876 picks = pick_types(evoked.info, ecog=True, seeg=True, dbs=True)
3877 evoked = evoked.copy().pick(picks)
-> 3878 frames = set(evoked.info["chs"][pick]["coord_frame"] for pick in picks)
3879 if not frames == {FIFF.FIFFV_COORD_HEAD}:
3880 raise RuntimeError(
3881 "Channels must be in the head coordinate frame, " f"got {sorted(frames)}"
3882 )
IndexError: list index out of range
File ~/projects/mne-python/mne/source_estimate.py:3930, in <listcomp>(.0)
3928 rrs = apply_trans(trans, rrs)
3929 else:
-> 3930 rrs = np.concatenate([s_rr[s["vertno"]] for s_rr, s in zip(surf_rr, src)])
3931 keep_all = True
3932 # ensure it's a usable one
IndexError: index 126967 is out of bounds for axis 0 with size 126967
Additional information
None
Description of the problem
Trying to use
stc_near_sensorsthere is one bug if there are any bad channels, that causesThis to fail with an index error because when
evokedgets picked the bad channels aren't included.There is another bug/API confusion that the default for
surfaceis'pial'so if you pass a volume source estimate and no argument forsurfacethen you get an index error because it tried to use the pial surface which has the wrong indices for your volume source estimate. That seems unnecessarily confusing, I think it should work reasonably with default arguments for both surface and volume source estimates.Also while doing a MWE, this link in the issue template is broken https://mne.tools/dev/overview/datasets_index.html.
Steps to reproduce
Link to data
No response
Expected results
Working stc
Actual results
Two index errors
Additional information
None