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:
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
