Hi Alastair,

I’m wondering how you ran mris_find_flat_regions? Is your output an annotation file?

mri_annotation2label will break an annotation file into multiple label files. Each label file contains R,A,S coordinates at the vertices of the specified surface. The default surface is 'white'. Other options include 'pial' and 'orig'. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label

Is that what you are looking for?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alastair Snell
Sent: Tuesday, September 5, 2023 4:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Voxel co-ordinates under pial surface patch

External Email - Use Caution

Dear Freesurfer experts,

After using mris_find_flat_regions to locate a flat patch on the pial surface, I now wish to extract the voxel co-ordinates of the volume within the cortex just below this flat region. Any ideas on how I can do this?

As always, any help is much appreciated.

Thanks,

Alastair