Hi Jake,
These are the steps which I perform to get a glass brain:
Required softwares - ITK snap, Paraview, BrainSuite (all of them are free).
1.) Segment brain from T1 MR using BrainSuite, the brain mask is in nifty format
2.) Use ITK snap to convert the brain mask to VTK format.
3.) Use Paraview to read in the converted brain mask (VTK) and then play around with the settings (lighting, specular, opacity) till I get a glass brain.
4.) To make a spherical ROI, I would use ITK snap, by having the T1 MR image (used for creating the glass brain) as a template. Create the ROI and export it as a VTK file.
5.) Open the ROI in Paraview (click the “eyes” to view the glass brain and the spherical ROI together) and play around with the properties, till you get your preferred image.
Hope it helps.
Cheers,
Lalith
> On Feb 2, 2018, at 5:05 PM, Jake Bowling <[log in to unmask]> wrote:
>
> Hello, does anyone know a way in SPM or elsewhere that I could plot ROI spheres in a 3d transparent/glass brain? Ideally, I would be able to manually enter MNI coordinates to center the sphere and then be able to adjust the sphere radius. End result might look something like this https://f1000researchdata.s3.amazonaws.com/manuscripts/7352/3edb985e-6158-43f2-8c38-0708421ec394_figure5.gif but with spheres.
>
> Thanks,
> Jake
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