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 ( 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
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* 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:
- 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
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
inbal paran