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Dear FreeSurfer developers,

First, thank you Douglas very much for your reply.

I have a follow up question, and for some reason I wasn't able to continue the thread, so I have copied the thread with Douglas's answer and my first question below.

Here is my followup question: I did the ROI analysis, asegstats2table and mri_glmfit with --table option as you suggested, but the thing is that I want to visualize my significant results using Freeview, how can I do that?

Also - by any chance can you tell me how can I continue the thread? When I am entered the archive I tried to click on "reply via email to.." but that just opens the outlook as a default and I don't work with outlook. For some reason I can't open the thread using gmail.

Thank you very much, Best, Inbal

Message: 7 Date: Fri, 8 Oct 2021 12:51:42 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] A question regarding a Freeview command To: freesurfer@nmr.mgh.harvard.edu Message-ID: bd3f5853-edf3-270d-9d1e-8c6f65d55420@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

The volume is the volume of cortex only, not the volume of subcortical structures. We don't have a VBM-style analysis that would be needed for subcortical GM. You can always do an ROI analysis, asegstats2table and mri_glmfit with --table option; this will allow you to analyze the volume of each structure as a single number, not a map. To answer your question, your freeview command line does not need to change.

On 10/4/2021 2:27 AM, inbal paran wrote:

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Dear FreeSurfer developers,

I am trying to run a group analysis to test for an association between *gray matter volume* and a behavioral measure of interest. reacon-all ran OK for all my subjects as well as mris_preproc followed by mri_surf2surf, and finally glmfit.? Finally, I wanted to visualize the significant voxels using freeview and followed the command line in the tutorial of the group analysis (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1vcxvE4KyDsi4qqXPfbLdF0-Ec-nWSe90uzyY86VVnWLhOo... <

https://secure-web.cisco.com/1_d3qazq-_19W6y1XEkeVPINXH5vgktFtuM1FrpU_HJNr44...

). However, since I am talking about volume and not surface, I wasn't sure how to edit the final command to visualize my results in freeview. I want to make sure it will include significant voxels both in subcortical + cortical regions. Should I use a stats.table file as an input? As you probably understand, working with Linux and FreeSurfer are both very new to me, if it's possible, any help would be greatly appreciated.

If it's relevant, these are the details of the version and platform I'm using:

1. FreeSurfer version:

freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.1 LTS 3) uname -a: Linux inbal-paran 5.11.0-37-generic #41~20.04.2-Ubuntu SMP Fri Sep 24 09:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) I also attached the mris_preproc log files in case it can help

Kind regards, Inbal Paran

-- *Inbal Paran, M.PT http://secure-web.cisco.com/1_uWMvw0JQHDbRb3qSmM-v2YM-E0oQrb6OCiSvXSQcDnOGybbgawoKOkmfiCdTjRH-7OghmS_9bhBq3B3mWpdtg_hTfAKr3muAEWw5VWMDiVSnhWcFYO6uxZq9TbL4elAEfVdXLMPyLwTqHYjOAxT4RE6yaZv7tCZIjqevI7ES-Lo4GqedoXasdLrxFAL9FFI3zjifYBX5KBXGi4YJHp9UcQGUAdOlbJPBXAl1uRORxB0ZPeLgOpO8qNU9MpXyajb/http%3A%2F%2Fm.pt%2F <

http://secure-web.cisco.com/1TCV1fAKzZJ5GOMgMi06jDdgf5mlDmrjtvqzBaNtTAOycuWe...

.

Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

Thanks again for your help, Inbal