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Thanks that worked perfectly.
Now that I have my flat patch how can I import it in matlab for some additional plotting?
Also, I read the wiki but I am not sure if and how I can import an atlas and create the annotation for the vertexes with that atlas.
Thanks
A
Il giorno mer 25 mag 2022 alle ore 16:19 Fischl, Bruce < BFISCHL@mgh.harvard.edu> ha scritto:
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.
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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.
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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
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