[Simnibs-discuss] Importing Brainsight Targets to SimNIBS - Target Seems Off

[Sliva, Danielle]

Hi Sean ,

Thanks for your response, please see below-

On Tue, Feb 7, 2023 at 5:30 PM Sean McBride <sean at rogue-research.com> wrote:

> On 24 Jan 2023, at 11:26, Sliva, Danielle wrote:
>
> > I am using SimNIBS4 to do a TMS simulation with targets from a previous
> > experimental session that utilized Brainsight for neuronavigation. I
> > followed the instructions here <
> >
> https://simnibs.github.io/simnibs/build/html/documentation/neuronavigation/brainsight.html?highlight=brainsight
> >
> > to import the targets from a Brainsight output text file, and chose the
> > *World* coordinate system (*NIfTI:aligned* was not an available option).
> >
> > The target I'm using is in primary somatosensory cortex, adjacent to the
> > motor hand knob. When I look at the simulation results in gmesh, it looks
> > like the coil position is off - it is in the correct general area, but
> way
> > too deep in the brain. The spatial distribution of the electrical field
> is
> > also too deep in the brain, without activation on the surface of the
> gyri.
> > I found the same issue for a different control target location.
> >
> > I used raw files (DICOM converted to NIfTI & DICOM) for SimNIBS and
> > Brainsight, respectively.
>
> You really should (in fact must) use the exact same dataset file with both
> SimNIBS and Brainsight.  I believe SimNIBS only supports NIfTI.  Brainsight
> supports NIfTI too.
>
>

I have already collected my data using Brainsight and am now trying to
import the targets to SimNIBS for modeling, so I cannot change the fact
that I used dicom files to create the targets (but, of course, will keep
this in mind for future experiments!). Since SimNIBS only supports NIfTI,
does this mean that it is not possible to use my Brainsight targets with
SimNIBS? Perhaps there is some kind of transformation I could do to the
Brainsight coordinates?



> > I know that Brainsight does some preprocessing to
> > the image (e.g. alignment to AC-PC line)
>
> Brainsight in fact does not do any such realignment.
>


For the preprocessing, I was just referring to the optional atlas
registration step in Brainsight.




>
> Cheers,
>
> Sean
>


Many thanks for your help,
Danielle



-- 
Danielle D. Sliva
PhD Candidate, Jones Lab
Dept. of Neuroscience
Brown University
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