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

[Oula Puonti]

Hi Martina,

1) Add the flag --forceqform at the end of the charm command and it
should work fine.

2) At the moment the neuronav integration is only implemented in python
unfortunately, so please use one of the example scripts provided on the
website: 

https://simnibs.github.io/simnibs/build/html/documentation/neuronavigation/softaxic.html

The simnibs neuronavigation import should automatically transform the
coordinates so that coil ends up in the correct location (and
orientation). However, please check that the coil looks to be in the
correct spot after running the simulation. The coil is automatically
visualized in gmsh so you should be able to see if there are any
obvious problems.

3) The optimized coil position (matrix) is printed at the end of the
.log file and is also stored in the .mat structure. The center
coordinate is defined by the first three numbers in the last column of
the matrix.

Best,
Oula





On Wed, 2023-02-01 at 16:51 +0100, Martina Mancano wrote:
> 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), 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). 
> 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). 
> 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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