Hi Alberto
Usually that means that you missed some cuts and there are still attachments. Occasionally it is due to a local minimum. You can try changing the distance preservation matrix to be bigger with longer range distances. Something like -distances
20 20 (out to 20 neighbors and 20 at each distance) or even largely. The defaults were set a long time ago when there was much less ram available. You can also try -dilate 1 to dilate the cuts by 1 vertex, although then you lose more of the surface
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Alberto Pisoni
Sent: Wednesday, May 25, 2022 5:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_flatten distortions
External Email - Use Caution
Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials.
see the result here.
Then I run the command
mris_flatten <input patch> <output patch>
from the surf dir and it works, but when I visualize the patch it is distorted, like if I did not cut the inflated surface.
What am I missing?
The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the system is a OS 11.6.1 BigSur Macbook Pro with M1 chip.
Thanks
Alberto
------------------------------------------------------
Alberto Pisoni, PhD
Associate Professor
Department of Psychology
University of Milano-Bicocca
Building U6 ~ Room 3139
piazza dell'Ateneo Nuovo 1
20126, Milano, Italy