wip

mne/gui/_ieeg_locate_gui.py

@@ -69,9 +69,7 @@ def _load_electrodes(info):
                 f'got {coord_frame} for {ch_name}. The easiest way is to '
                 'use saved locations from this GUI. You may want to solve '
                 'previous channel locations having the wrong coordinate '
-                'frame by removing them with '
-                '`inst.set_montage(mne.channels.make_dig_montage(None), '
-                'on_missing="ignore")`')
+                'frame by removing them with `inst.info["dig"] = []`')
             chs[ch_name] = ch_coord
     return
 

tutorials/clinical/10_ieeg_localize.py

@@ -208,13 +208,28 @@ def plot_overlay(image, compare, title, thresh=None):
 # load electrophysiology data
 raw = mne.io.read_raw(op.join(misc_path, 'seeg', 'sample_seeg_ieeg.fif'))
 
-ch_coords = np.array([ch['loc'][:3] for ch in raw.info['chs']])
+# load electrode positions from file
+elec_df = pd.read_csv(op.join(misc_path, 'seeg', 'sample_seeg_electrodes.tsv'),
+                      sep='\t', header=0, index_col=None)
+ch_names = elec_df['name'].tolist()
+ch_coords = elec_df[['R', 'A', 'S']].to_numpy(dtype=float)
 
 # create symbolic link to share ``subjects_dir``
 seeg_subject_dir = op.join(subjects_dir, 'sample_seeg')
 if not op.exists(seeg_subject_dir):
     os.symlink(op.join(misc_path, 'seeg', 'sample_seeg'), seeg_subject_dir)
 
+# get fiducial points for our subject from the Talairach transform
+# the was computed during the Freesurfer recon-all
+lpa, nasion, rpa = mne.coreg.get_mni_fiducials(
+    'sample_seeg', subjects_dir=subjects_dir)
+lpa, nasion, rpa = lpa['r'], nasion['r'], rpa['r']
+
+# create a montage in subject-specific brain space
+ch_pos = dict(zip(ch_names, ch_coords / 1000))  # mm -> m
+montage = mne.channels.make_dig_montage(
+    ch_pos, coord_frame='mri', nasion=nasion, lpa=lpa, rpa=rpa)
+
 ###############################################################################
 # Let's plot the electrode contact locations on the subject's brain.
 
@@ -223,7 +238,7 @@ def plot_overlay(image, compare, title, thresh=None):
     op.join(misc_path, 'seeg', 'sample_seeg', 'mri', 'brain.mgz'))
 
 # get native to head trans
-subj_trans = mne.channels.compute_native_head_t(raw.get_montage())
+subj_trans = mne.channels.compute_native_head_t(montage)
 
 # set new montage
 raw.set_montage(montage)