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:
>
> ????????External Email - Use Caution
>
> 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*
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://freesurfer.net/fswiki/FsTutorial/GroupAnalysisV6.0
> <https://secure-web.cisco.com/1_d3qazq-_19W6y1XEkeVPINXH5vgktFtuM1FrpU_HJNr44_3uuNvlnNfQqepHBhMKZsl9biOcmanOYEOsi5frjSB9zVZk8SeuQj5IayujrPskSPaV_zisvFp29GavDmi9FN7EGTVyLcedxcvBPYIh4YdE1wpQ9S1ahGYHbKo5fXBOMPe4Eujx-adkDYxFJnzdlt8OvwBeDaFxQqVdeOD7OpK54HEfuLrSEUe_5t224wDsiKSZpvJd_k9IiEu43Jgl_M_rTPJZ9BkEsjkWfBKzg/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0>).
> 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/1TCV1fAKzZJ5GOMgMi06jDdgf5mlDmrjtvqzBaNtTAOycuWedE4vC_1UvecqwIebSkbIU3h5PEZFwNVgOOI0Lcz14FEkLqJnJ8ImbQSgRNAPPNlbJPJOqQNIv12LcWCKNxRPll3BIR89wAcD3kb3hsf9o85NhgI40g8Pk6sGw7RE1MpjPg1itpIG_RX4fvqJVT2K0zVIBwhcKecZiOhrc-3QJrVCLRmhkVy3yhcYptd9aRP2EZG3TPMQAo-M3lwix2CWbeZePHLE3XQCpIQoYYg/http%3A%2F%2FM.PT>.
> *
> 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