Saving annotation to file

[iamjoostjanssen]

Hi,

We're using vis.subject.annot() to save custom annotations. Supposedly, a custom annotation is made (using freesurfer tools?) and this is saved to an image. Would it be possible to also output the custom annotation (in gii or cifti or .annot) and not just it's image?

Thank you for the great tool!

-joost

[dfsp-spirit]

Hi, could you give me an example function call of what you are doing? I have an idea but I want to be sure. I will have a look, and I guess it should be possible to do that.

[dfsp-spirit]

Basically an annotation is just a long list of integers, one per vertex in the brain mesh, where each integer represents a region (e.g., 1=region1, 2=region2, and so on). The order of the list corresponds to the vertex list, so a list of 4,7,7,... would assign the first vertex region code 4, the second and third vertex region code 7, and so on. If needed, you can assign a color to each code for visualization.

That being said: yes, it is possible to do what you want. Use the functions freesurferformats::write.fs.annot() and freesurferformats::write.fs.annot.gii(). As the freesurferformats package is a dependency of fsbrain, you already have it installed.

Unless you have more questions, I would close this as solved next time I iterate though here.