When you run the thickness analysis with multiple comparisons correction (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the significant areas. You can use this to extract other information. If you want volume, then run mris_preproc using the --meas volume flag, the apply the ocn to this file using mri_segstats using the --avgwf and --accumulate flags (and --exclude 0). This will give you a nsubjects-by-nclusters text file where each entry is the volume for that subject/cluster

On 12/8/2020 10:48 AM, Sara Lyn wrote:

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Hi Joceyln,

I'm not trying to run a new group analysis but want to extract volume values from significant thickness ROIs obtained from a thickness group analysis. 

Thank you

Sara

On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. <JSMORA@mgh.harvard.edu> wrote:
Hi Sara,

You may want to try --meas volume in place of --meas thickness when running mris_preproc. 

I would also recommend looking at our ROI Analysis tutorial and Volumetric Group Analysis tutorial. Please let us know if you are still having trouble.

Cheers,
Jocelyn
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sara Lyn <saralyn543@gmail.com>
Sent: Monday, December 7, 2020 10:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] group analyses
 

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Hi FS developers,

I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) for a surface based thickness group analysis. I am trying to extract volume measures from the same significant thickness ROIs. Is there any way to do this? Thank you!

Sara 
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