tms-head-recon

Some freesurfer magic and MNE viz

Some notes to figure out how to show TMS stim sites scalp/skull surfaces w/ promixity to particular regions in the brain

General ideas

• use freesurfer to generate scalp/skull surfaces from T1 MRI
• use mne tools to generate BEM surfaces from freesurfer outputs
• use mne to visualize TMS coil positions relative to scalp/skull/brain surfaces and/or matlab with specific freesurfer visualization tools

1. Assuming you have run freesurfer’s recon-all on your T1 MRI to generate the necessary surfaces and have installed mne tools on your machine + have matlab knocking around 😄!

2. Use mne watershed_bem to generate scalp and skull surfaces

SUBNAME=subject-A
mne watershed_bem -s ${SUBNAME}

and visualise:

SUBNAME=subject-A
mne freeview_bem_surfaces -s ${SUBNAME}

This will allow you to get some nice screengrabs of skull / skin surfaces. Etc.

I also used this to approximate the inion/nasion points on the scalp surface for Cz locating. See code to check if that makes sense

Visualizing TMS coil positions w/ CZ etc.

Probably easiest to do this in python using mne.viz. Here’s some example code to get you started h/t prompts from Claude in Visual Studio Code and the documentation on the MNE site.

1. Make sure the right python environment is activated with mne installed

# if you used the MNE installer, something like:
conda activate /Applications/MNE-Python/1.11.0_0/.mne-python

You should be able to run the interative viz code below and see the scalp/skull surfaces along with fiducials and Cz of montage, if I got that correct. Inspect code at to see details.

# make sure right python!
conda activate /Applications/MNE-Python/1.11.0_0/.mne-python

# then run
python ./create_montage_viz.py

Etc. etc…

Penalty for particular paths

• code includes a penalty for paths that deviate from sagittal plane x_dev is penalized.
• to avoid the shorted path hugging the surface inferiorly (when skull/scalp surfaces are relatively clipped inferiorly), a penalty for low z values (when z_pos is negative) is included.

# default behaviour PREFER upwards paths
python create_montage_viz.py    # default behaviour
python create_montage_viz.py up # default behaviour

# as a reality check you can also try to penalise upwards paths by PREFERing downwards paths
python create_montage_viz.py down

Paths generated with preference for up (left) or down (right) directions