[Simnibs-discuss] Error message creating head mesh - Softaxic coordinates compatibility - TMS optimization

[Martina Mancano]

Hi,

It's my first time approaching SimNIBS, and I have three main questions:

1) I'm trying to create a head mesh .msh from a .nii T1 file from the
command prompt (following the instructions I found here
<https://simnibs.github.io/simnibs/build/html/tutorial/head_meshing.html#>),
but it gives me the same error message, and it stops the procedure:

[ simnibs ]CRITICAL: Uncaught exception

ValueError: The qform and sform of do not match. Please run charm with the
--forceqform option

and I don't know what does it mean/how to solve it.

2) I was wondering whether I can use SimNIBS to optimize TMS coil
positioning, in conjunction with Softaxic neuronavigation. I see that you
provide a script to import coordinates from .stmpx files generated from
Softaxic (here
<https://simnibs.github.io/simnibs/build/html/documentation/neuronavigation/softaxic.html>
).
A.  Does it run on Python? Is there any Matlab version I could use?
B. Is the coordinate system used by SimNIBS compatible with Softaxic?
.stmpx contains points acquired in Softaxic in different coordinate
systems, which one is the SimNIBS compatible one?

3) I tried to do the TMS optimization following the tutorial on the data
you provided (here
<https://simnibs.github.io/simnibs/build/html/tutorial/tms_optimization.html#tms-optimize>
).
I have different output files (.msh, .opt, .geo, etc), but I'm not sure
where I can find the coordinates of the optimized coil position.

Thanks in advance,

Best,

Martina Mancano
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