External Email - Use Caution 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" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] A question regarding a Freeview command To: freesurfer@nmr.mgh.harvard.edu Message-ID: <bd3f5853-edf3-270d-9d1e-8c6f65d55...@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* > https://secure-web.cisco.com/1vcxvE4KyDsi4qqXPfbLdF0-Ec-nWSe90uzyY86VVnWLhOo6DdSS9uWRz-jiT2_Krrn0Py4dzxzdGziKflUP4IHma4BKS0q8gr0JI2iv8X3nEG6mYLGzRjZAmV_rej74Pnk-n0GlFsJyUouPWoAPRnj-53YyI8NRhGSkLyCmpuCdPLdgodIuUw28a-CESw1MpS45sY1xgJCByHCWCPi8qQOAhJmImtOUlkKYTK6rcf5Ey37gCZYkhUOSgJpEmX5O0/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0 > < 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/1_uWMvw0JQHDbRb3qSmM-v2YM-E0oQrb6OCiSvXSQcDnOGybbgawoKOkmfiCdTjRH-7OghmS_9bhBq3B3mWpdtg_hTfAKr3muAEWw5VWMDiVSnhWcFYO6uxZq9TbL4elAEfVdXLMPyLwTqHYjOAxT4RE6yaZv7tCZIjqevI7ES-Lo4GqedoXasdLrxFAL9FFI3zjifYBX5KBXGi4YJHp9UcQGUAdOlbJPBXAl1uRORxB0ZPeLgOpO8qNU9MpXyajb/http%3A%2F%2Fm.pt%2F> > < 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 -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1GATqktVB9GCv-D6rmlzLZKLrLOjzGIDyvhTd6-WnB7r0cQb3yvtdFIwpHcWlnCh_d1FHApujEx-Pxe3zkiBiVtmWQKysFy8JcConl8NX6NgVZOAO4o3RvnhRU-O_qywOp1A2rL0UVU0tkFH9lnqoK5yzmHxc85QbY_rNdOVAdMPYSM0BeHNLaZ0PlTS2KxQhRbWvRa6GjVBk4GtoOAk5DreaSA23vx6zkQc06IRrYu3KdcbftsrEgIPkJlNpOEZx/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.
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