you can try $FREESURFER/matlab/read_patch.m
On 5/25/2022 5:02 PM, Alberto Pisoni wrote:
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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
<bfis...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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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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