Hi Daniel

The patches are a somewhat different format than surfaces, so you need to load the surface that you cut it from first, then load the patch afterwards. I would think you could flatten anything if you have the right files in the right places (like the smoothwm as you mentioned)

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Glen, Daniel (NIH/NIMH) [E]
Sent: Friday, April 18, 2025 5:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_flatten limitations

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I would like to abuse mris_flatten with a non-cerebrum surface. Will this work? It works for a sphere, but if I make cuts on more complicated shapes, it fails after hundreds of iterations with a "Segmentation fault". Are there any special tricks? Each patch file of cuts requires a different ?h.smoothwm file or h?.smoothwm file. If I copy the original surface to that requested file, the program continues. Is this correct? How can I predict this? I did manage to get one to make a flat.3D file, but display in Freeview or info from mris_info fails for that output, first using up large amounts of memory then crashes with another segmentation fault .

Thanks,

Daniel