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

[Sliva, Danielle]

Thanks, Sean.


On Wed, Feb 8, 2023 at 12:34 PM Sean McBride <sean at rogue-research.com>
wrote:

> On 8 Feb 2023, at 11:25, Sliva, Danielle wrote:
>
> > 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
>
> Ah, I see.
>
> > Perhaps there is some kind of transformation I could do to the
> > Brainsight coordinates?
>
> Probably the best is, when you export the Targets/Samples to .txt file
> from Brainsight is to use "Brainsight" coordinates.  "Brainsight"
> coordinates are DICOM-style where the origin is at RAI (and the vectors
> point towards LPS).  I believe the SimNIBS importer supports such
> coordinates too:
>
>
> https://simnibs.github.io/simnibs/build/html/documentation/neuronavigation/brainsight.html?highlight=brainsight



I just tried this, and unfortunately the importer doesn't support
DICOM-style coordinates.


*"ValueError: Coordinate system 'Brainsight' is not supported. Export
targes/samples as NIfTI:Scanner (or Dicom/World)."*


>
>
> Note that the upcoming Brainsight 2.5 will also be able to import/export
> .txt files where the origin is at LPI (and the vectors point towards RAS).
>
>
Looking forward to Brainsight 2.5!


> >>> 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.
>
> Even that feature though does not actually process/realign the project's
> dataset, unlike some other software.  It merely creates an internal 4x4
> matrix to map between the dataset's coordinates and MNI coordinates.
>


Oh, good to know :)



>
> Cheers,
>
> Sean
>


Thanks again,
Danielle


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