MNE version: 0.24.1
operating system: Windows 10
Platform: Windows-10-10.0.19043-SP0
Python: 3.9.9 | packaged by conda-forge | (main, Dec 20 2021, 02:36:06) [MSC v.1929 64 bit (AMD64)].
Executable: C:\anaconda3\envs\mne\python.exe
CPU: Intel64 Family 6 Model 151 Stepping 2, GenuineIntel: 24 cores
Memory: 31.7 GB
mne: 0.24.1
numpy: 1.22.0 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy: 1.7.3
matplotlib: 3.5.1 {backend=QtAgg}
sklearn: 1.0.2
numba: 0.53.1
nibabel: 3.2.1
nilearn: 0.8.1
dipy: 1.4.1
cupy: Not found
pandas: 1.3.5
mayavi: 4.7.2
pyvista: 0.33.2 {OpenGL 4.5.0 NVIDIA 512.15 via NVIDIA GeForce RTX 3090/PCIe/SSE2}
pyvistaqt: 0.7.0
ipyvtklink: Not found
vtk: 9.0.3
PyQt5: 5.12.3
ipympl: Not found
mne_qt_browser: 0.1.7
pooch: v1.5.2
I am working on a tutorial on āLocating intracranial electrode contactsā and have two problems. The first is the creation of the lh.seghead file required for Head->MRI conversion, and the second is the creation of the Montage file used for positioning to the standard brain.
The MNE sample has a file called lh.seghead (in MNE-misc-data\seeg\sample_seeg\surf), but it is not in the data generated by Freesurferās recon-all.
I know from the notes that it is possible to create them by using mne.bem.make_scalp_surfaces, but I donāt know how to use it.
I donāt know how to use it (I canāt find any reference to it), so I canāt create it.
RuntimeWarning: seghead
not found, skipping head plot, see :ref:mne.bem.make_scalp_surfaces
to add the head
gui = mne.gui.locate_ieeg(raw_ecog.info, subj_trans_ecog, CT_aligned_ecog,
I think the second is related to the first.
The calculation and definition of the Matrix to be converted to Head->MRI is done in the first calculation.
You need to use that Matrix(subj_trans_ecog) when aligning to the standard brain.
subj_trans_ecog = mne.coreg.estimate_head_mri_t(āsample_ecogā, op.join(misc_path, āecogā))
I skipped it for now, since the first one was just noted, but
I canāt confirm what effect this way would have on the next analysis.
If I position it to the standard brain as is, I get the following error.
-āmontage.apply_trans(subj_trans_ecog) Problem line
AttributeError: āNoneTypeā object has no attribute āapply_transā
Since the problem with Montage is also in the coordinate system conversion between Head and MRI, we think that the creation of the first lh.seghead file is important.
(1) Function, impact and creation method of lh.seghead
(2) How to create Montage in ECoG data of Nihon Koden (currently using mne.channels.make_dig_montage())
I would appreciate any information on the above two points.