Hello,
I'm trying to generate surface meshes for different brain regions that can be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, etc.). I ran recon-all on my T1 images, and the parcellation/segmentation looks fine. However, I noticed that when I imported this data into 3DSlicer, the volumes of these regions did not match the volumes in the aseg.stats file. In some cases, the differences were quite substantial. I tried removing all smoothing filters in 3DSlicer but the outcome was the same.
Do you know what could be going wrong here? Alternatively, is there an easier way to generate surface meshes from the aparc or aseg atlases?
I'm using the ICBM 2009c Nonlinear Asymmetric template ( http://nist.mni.mcgill.ca/?p=904) as a generic brain volume (though alternative suggestions are welcome).
Thanks! Jonah