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Hi Alastair,
I have never used mris_find_flat_regions.
Looking at the program, here is usage of the program:
mris_find_flat_regions [-s min-vertices-required] [-t threshold]
<input-surface> <output-file>
I think you can try -s option. It should segment surface into ROIs with at
least min-vertices-required vertices. The output is an annotation file for this
option.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Alastair Snell
Sent: Monday, August 14, 2023 9:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mris_find_flat_regions help
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to locate flat regions along the pial surface of an MRI scan,
ideally about 5mm in size. I am using mris_find_flat_regions in order to do
this. Unfortunately, the information page (MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1Nl9fyCfxS_F0MNWvKMDvI4Qn9OW0oPXh07Da00laU0_J8fO4nt57x8bh5JT3rVwCsBr-nfRRP2qFmi4cHaLV2ooM-2IV-FsoQEFtVhjaVv9g96gGqn-3SMe2FPW0iZG8cp_14lP3pap4EAiGzR0yzsiMoJSDn8eWzFb42nS3KnW8b7Rbaj_HyxZapKIYUrtVeIAt_9Nj7g_Hy8C9DJQv38WK-NQuuJYjvkKXv2CD_oGHbY_9MXVjr8Pw4ZulyXmY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_find_flat_regions<https://secure-web.cisco.com/1NI_7_9GXEGWvnwy1GzFMB4NGJEbyzBihtm4Wzlv7x59Qo2TfK5OnUEXXwam91Ng3R6XxgIO5ms_Qk8OCgvXkUobTBXA4O7w-tHq5D72lvImTwQEiMNAdjHFDZ6-hrILlG6b0qnuXaRhAACG7vLjyx6VgGEIsvL2BKP_sECFZOGvUjwd7YTkQRsM1MeAY1XSoz0GOY1rGoXCFQhplbl9lVzMPt-3iuwmubazpiKCoD5s7yWTotizjpuy9aguW59YR7NZNxEunbUlsUfZ-h5SnwIWmHg4cx20VxQyTJLbaY1ENyZ2jg7EsruzhTDODSODgrYleUmz4a6Q_CoDLgSe0VQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_find_flat_regions>)
isn't informative enough for me to solve my issue.
I have used the command on lh.pial in the good_output folder located in
buckner_data of the tutorial data set. This returned lh.pial.flat.w. I used
mris.convert to convert this into lh.pial.flat.asc - which is a series of
vertex numbers on the left column and a column of 1's on the right. I want to
be able to visualize these regions in freeview (tksurfer does not work at my
institution), cluster them into local groups (patches) of vertices, and export
one of these clusters/patches as a set of co-ordinate vertices.
I've searched the list and no similar issues have been reported. Does anyone
have any thoughts on how to achieve this?
1) FreeSurfer version: freesurfer 7.3.2 (linux)
2) Platform: Linux Ubuntu 22.04
3) uname -a: Linux wks6 5.19.0-46-generic #47~22.04.1-Ubuntu SMP
PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
Many thanks in advance,
Alastair Snell
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