I am trying to make a brain hull surface of the brain using 3dSkullStrip and IsoSurface. I have a stripped brain but my isosurface output is giving me a square plane (image attached).

I entered: isosurface -input Rose3D_stripped.nii -isoval V
I got warning: Warning SUMA_Make_Edge_List_eng: You have edges that belong to more than two triangles. Bad for analysis assuming surface is a 2-manifold.
But still got the output file: isosurface_out.ply

Why am i getting this warning? And why is my output file not showing the shape of the brain?


That warning is actually common.

  1. Can you display normal surface data in suma?

  2. Are you sure that the input dataset is really zero
    outside the brain? What is the output of this?

3dhistog -nbin 20 Rose3D_stripped.nii

  • rick