Plotting subcortical data

1

Hi all,

I am currently trying to plot subcortical results onto a surface. I have create a *surf.gii file of the subcortex based of my atlas (harvard-oxford subcortex atlas). However, I don’t know how I can then plot the values for each ROI onto the surface, I currently have a matrix that contains a value for each ROI, but I cannot translate this into a volume or surface file?

Appreciate anyone’s feedback or advice on programs that could do this for me.

2

You can try and use Nilearn routine for volume-to-surface projection.
https://nilearn.github.io/modules/generated/nilearn.surface.vol_to_surf.html
Best,
Bertrand

3

You may want to try Surfice.

  1. Choose Scripting/Python/MatcapSubcortical to see an example of how you can make the cortex mesh translucent to reveal the subcortical mesh.
  2. Choose Scripting/Python/HideCurves to choose the “HideCurves” shader, which hides cortical sulci (viewpoint independent).
  3. Choose Scripting/Python/HideCurves and then change the Shader pulldown menu from “HideCurves” to “Outline” - this hides cortical surfaces that are not parallel with the line of site (a viewpoint dependent cutaway).
  4. Choose Scripting/Python/HideCurves and then change the Shader pulldown menu from “HideCurves” to “Grid” - this only shows the cortical surface along grid lines, with the sliders allowing you to choose the grid spacing and thickness (viewpoint independenty).

subcortical
subcortical1842×1271 304 KB

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4

Thank you Chris! This is really useful.