# be ``1`` s, the second ``2`` s and so on. This image can then be warped by
# the SDR transform. We can finally recover a position by averaging the
# positions of all the voxels that had the contact's lookup number in
# the warped image.
# first we need our montage but it needs to be converted to "mri" coordinates
# using our ``subj_trans``
montage = raw.get_montage()
montage.apply_trans(subj_trans)
# higher thresh such as 0.5 (default) works when `zooms=None`
montage_warped, elec_image, warped_elec_image = mne.warp_montage_volume(
montage,
CT_aligned,
reg_affine,
sdr_morph,
thresh=0.1,
subject_from='sample_seeg',
subjects_dir_from=op.join(misc_path, 'seeg'),
subject_to='fsaverage',
subjects_dir_to=subjects_dir)
fig, axes = plt.subplots(2, 1, figsize=(8, 8))
nilearn.plotting.plot_glass_brain(elec_image, axes=axes[0], cmap='Dark2')
fig.text(0.1, 0.65, 'Subject T1', rotation='vertical')
nilearn.plotting.plot_glass_brain(warped_elec_image,
axes=axes[1],
cmap='Dark2')
fig.text(0.1, 0.25, 'fsaverage', rotation='vertical')
fig.suptitle('Electrodes warped to fsaverage')
del CT_aligned
# a lookup table of the electrode contacts. In this image, the background will
# be ``0`` s all the bright voxels near the location of the first contact will
# be ``1`` s, the second ``2`` s and so on. This image can then be warped by
# the SDR transform. We can finally recover a position by averaging the
# positions of all the voxels that had the contact's lookup number in
# the warped image.
# first we need our montage but it needs to be converted to "mri" coordinates
# using our ``subj_trans``
montage = raw.get_montage()
montage.apply_trans(subj_trans)
montage_warped, elec_image, warped_elec_image = mne.warp_montage_volume(
montage,
CT_aligned,
reg_affine,
sdr_morph,
subject_from='sample_seeg',
subjects_dir=subjects_dir,
thresh=CT_thresh)
fig, axes = plt.subplots(2, 1, figsize=(8, 8))
nilearn.plotting.plot_glass_brain(elec_image, axes=axes[0], cmap='Dark2')
fig.text(0.1, 0.65, 'Subject T1', rotation='vertical')
nilearn.plotting.plot_glass_brain(warped_elec_image,
axes=axes[1],
cmap='Dark2')
fig.text(0.1, 0.25, 'fsaverage', rotation='vertical')
fig.suptitle('Electrodes warped to fsaverage')
del CT_aligned