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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'. https://secure-web.cisco.com/1RhoYONhPYWjzvAXirf2sfiS4Trw3AX8iLe0q2yps6U5AZa...

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