Dear Angelique I’m not a 3DSlicer expert but you can extract the regions with mri_extract_region, turn them into stl meshes with mri_mc, and possibly smooth them a bit with mris_smooth Cheers, /E
Juan Eugenio Iglesias http://www.jeiglesias.com
On Sep 24, 2022, at 16:15, Paulk, Angelique C.,PHD <APAULK@mgh.harvard.edumailto:APAULK@mgh.harvard.edu> wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer