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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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_J8f...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