Visualizing cortical activation with scalp overlay


I am looking to visualize surface activation with a (transparent) scalp mesh stl file overlaid on top. I have been using SUMA to view cortical activation so far. What is the recommended way to do this?


You can either add the scalp surface to your spec file, making sure the scalp has the same “state” as other anatomical surfaces or you can have suma load requested surfaces on the command line.

suma -onestate -i surf1.gii surf2.gii scalp.stl

Great. When loading requested surfaces on the command line, is there a way to make the scalp surface transparent?

Select the transparency of the scalp surface in the surface object controller undre “trn” or Ctrl-o to cycle among the transparency/opacity settings for just that surface.

Perfect thanks. And lastly, how can I resolve alignment issues between the pial.gii files and the scalp.stl file?

We don’t have a nudging or alignment tool for this, but ConvertSurface can apply transformations. Shifts are the last column of the matrix input.