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Hi Len,

As I understand it, .annot file is surface overlay for cortical surface parcellation.

I’m trying to understand what you mean by “volumetric aparc.annot”. How did you obtain the file?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Len Jacob Sent: Tuesday, April 18, 2023 2:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Loading and editing volumetric .annot in Matlab

External Email - Use Caution Dear Freesurfer enthusiasts,

I would like to load a volumetric aparc.annot file into Matlab with the goal of editing the color information for certain ROIs in order to convey some group-level results in the subcortex.

I've previously done this for cortical surfaces by loading lh.aparc.annot (and rh.aparc.annot), but I now need to convey surbcortical results, and read_annotation does not work for the volumetric aparc.annot. I assume write_annotation would not work either.

All the information I have been able to find relating to modifying a .annot and creating custom colortables has been for surface data. Any help in getting this done in the subcortex would be appreciated.

Best regards, Len

-- Leandro P. L. Jacob, Ph.D. (he/him) Postdoctoral Associate at the Lewis Lab Biomedical Engineering Department, Boston University