Smoothing an isosurface

AFNI team,
I am trying to represent brain masses as separate surfaces in their native space along with the pial surface. I used the afni drawing tool to draw out each mass and then used IsoSurface -input drawnfile -isoval V -mergerois -o_fs output_surf to create the surfaces. I am representing these objects in freesurfer space so I’ve had to apply a transformation matrix to the ouput ascii file. Is there a way I can smooth the drawn mass surface so that it looks cleaner? If this is possible, is there a way I can do that with my modified ascii file or do I need to start the process from the .brik output of the drawn rois?

Thank you for your help,


Hi, Patrick-

The “-Tsmooth KPB NITER” option to IsoSurface controls the smoothing/polishing of the created surface: KPB kind of controls the polishing strength (bigger is more agressive polishing) and NITER is the number of iterations. You can add more iterations, or increase KPB to make the output smoother.

I do think you’d have to re-run IsoSurface to do this. Here is a script example of doing that, as well as of visualizing the output:


OK! I will check that out, thank you for your help