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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claiming to be
https://drive.google.com/file/d/11co39jCDmQC8VdLrN6iQp-ytWxxz40WY/view?usp=sharing<https://secure-web.cisco.com/1xjf27LYk5Ie25CTk51Q3cPiwVe-uMjYXB4V0ViZqlanRh7HkTXKDS-1HTcTPXJCxmT3JtXYt-sqlqTYba3y3B2xlT0j5KYd9OUxIUWG4M1l2bD8eJiwJyFN7ULqtMaNqcShZD1j9pfoIDMHkPwLQXeQzBegTua5cg8XJj2IQzIAXpclV-iPlS4zJyPVcu0aZPVRHZpbR59kD4h0kNhV2r27EjnaJQnz6gwXtHebd3zAt9zul6Da9a81ExBbcVBsSEkuKIo56Bk4UAeG4zUFxUaqXh3VdUOKAuLe3rW_KxvppnVmzzBTGolW24VY3i2YqGx-T0DeBXUqluMeJ1ZOfp3e6RoAONlmXcMMUMmP40Ng/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11co39jCDmQC8VdLrN6iQp-ytWxxz40WY%2Fview%3Fusp%3Dsharing>
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.
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://drive.google.com/file/d/11cOYRjQqXsyPoIly3WiMPVT7vYBK5vFw/view?usp=sharing<https://secure-web.cisco.com/128ktBKDV9wlBus-Bu1XsphHIMQpHtnuoTRQ6748JzsrgK9lPn_h05GfjIBjSL-QA4cPUy-IFGDhAUETl-kUeOrwC9-ZtdJAVVuZHIDhbFmXrSVogZpjuArXlFgXwcp8YVysQrS1qnDMwIjtXsob18Ruuc-p_jXrL-hKdZXCjWieJ09HVkdLTixeRmLvq-LtP3II8nyipaXht-odxS8YqLRWQLoDV0ra6ge_Vg7HK6AfOM2XAtiAc9PykwlNBwPk9pu5NXGXpPdnAH8RH2h2IrdfshzGVdJgp1mLcOrZj-eoDf1dgP5P3xFHm_ZMuExHuYn801IRrIlJzaJGY9yqhwHiVy6LNQNwDaZqNerVElaE/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F11cOYRjQqXsyPoIly3WiMPVT7vYBK5vFw%2Fview%3Fusp%3Dsharing>
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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