Hello,
I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a
number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz"
file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview.
Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export?
Thank you for all your help,
Angelique
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