[Simnibs-discuss] How to define matsimnibs?

Deborah Klooster Debby.Klooster at UGent.be
Fri May 6 20:53:53 CEST 2022

Dear simNIBS experts,
I would like to run a simulation (so no actual stimulation performed yet!) of TMS induced electric field after DLPFC stimulation, targeting particular MNI coordinates within the gray matter, with the coil positioned tangentially to the scalp with the handle pointing backwards in a 45-degrees angle with the A-P line. Specifically, I have three questions about how I can define my position and orientation properly (or in other words: what is the best way to define my matsimnibs?):

1.     I know my stimulation target in the gray matter and I know simnibs has an ‘project on scalp’ function built in. I assume that this basically seeks the nearest point on the scalp? Can we get the information (i.e., coil position on the scalp based on gray matter position input) somewhere out of the code? It must be in there somewhere but I failed to find it…

2.     I am struggling with the left-upper 3x3 part of the affine transformation matrix. I know the rotation around the z-axis is 45 degrees but I am not sure how to define the rotation around x and y (in order to keep the coil tangentially to the scalp). I could derive these rotations from a vector normal to the scalp (I think this would just be an extension of the projection from the gray matter point to the scalp position?). Should I derive this normal vector from curvature data from freesurfer or is it possible to retrieve this info in a simpler way?

3.     Assuming that, at some point, I will manage to define matsimnibs, is there a proper way to visualize this (preferable in the simnibs GUI) such that I can verify if my matrix, and hence my subsequent simulation, is correct? What is the relation between the matsimnibs and the reference coordinates that need to be put in the simnibs GUI as direction reference?
Thank you very much in advance!
Kind regards,
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