On Sep 23, 2020, at 4:57 PM, Sanchez, Justin <Justin.Sanchez@MGH.HARVARD.EDU> wrote:

Hi FreeSurfer team - 

Hope all is well with you these days!

I am trying to pull off the following: 

Given a list of vertices that mark the outline of a new surface ROI (e.g., a path file, attached) and other FS surface files,

  1. Make a closed path through these vertices

  2. "Fill" the closed path to create a new label

  3. Save the new label

This is basically the process outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit#Actuallycreatingthenewregion, except that the initial boundary vertices/path file are identified automatically (by an algorithm) rather than manually clicked.

This works great if I load the surface in tksurfer, then load the path, then do custom fill, etc. But I’d love to be able to do this automatically, for many subjects, without having to load tksurfer. 

Since this functionality is implemented in tksurfer it seems there must be code for it, but I can’t find it in the FS docs or mailing list history. Can you help with this? 

Thanks a bunch,

Justin

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