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thanks alot Yujing for your answer.
I changed the SUBJECTS_DIR to my external hard drive before began the analysis by the code: SUBJECTS_DIR='pwd'

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Yunus Soleymani

Ph.D. Candidate of Neuroimaging 
Tehran University of Medical Sciences

+98 914 526 9298
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On Wednesday, November 29, 2023 at 04:35:14 PM GMT+3:30, Huang, Yujing <yhuang43@mgh.harvard.edu> wrote:


Hi Yunus,

 

‘fsaverage’ is an average subject comes with Freesurfer distribution in $FREESURFER_HOME/subjects/. fsaverage is a template brain based on a combination of 40 MRI scans of real brains. It can be used as a common space for group comparison.

 

What is your SUBJECTS_DIR? You should not set SUBJECTS_DIR to $FREESURFER_HOME/subjects/.

 

You should see ‘fsaverage’ as a symbolic link in your SUBJECTS_DIR.

 

Best,

 

Yujing

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of yunus soleymani
Sent: Wednesday, November 29, 2023 5:54 AM
To: Freesurfer Support List <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] fsaverage folder

 

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Hello Freesurfers,

 

I am currently using the parallel recon-all code in Freesurfer to analyze my subjects. While reviewing the results folder, I came across a folder named 'fsaverage' which had a locked icon next to it, along with the folders for each individual subject. I am curious to know what this folder is and how it could be useful.

 

Thank you for taking the time to answer my question.

 

Best regards,

Yunus

 

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