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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' --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus@yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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

#yiv5545478884 filtered {}#yiv5545478884 filtered {}#yiv5545478884 filtered {}#yiv5545478884 filtered {}#yiv5545478884 filtered {}#yiv5545478884 p.yiv5545478884MsoNormal, #yiv5545478884 li.yiv5545478884MsoNormal, #yiv5545478884 div.yiv5545478884MsoNormal {margin:0in;font-size:11.0pt;font-family:sans-serif;}#yiv5545478884 a:link, #yiv5545478884 span.yiv5545478884MsoHyperlink {color:blue;text-decoration:underline;}#yiv5545478884 pre {margin:0in;font-size:10.0pt;}#yiv5545478884 span.yiv5545478884HTMLPreformattedChar {font-family:Consolas;}#yiv5545478884 span.yiv5545478884EmailStyle21 {font-family:sans-serif;color:windowtext;}#yiv5545478884 .yiv5545478884MsoChpDefault {font-size:10.0pt;}#yiv5545478884 filtered {}#yiv5545478884 div.yiv5545478884WordSection1 {} 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.eduOn 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

External Email - Use Caution

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

-------------------------------------------------------------------------------- Yunus Soleymani

Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences   MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus@yahoo.com+98 914 526 9298 --------------------------------------------------------------------------------   _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1J14i_ilaSpKcuP4owBeji4zU8o-Hi06ZukvdnhcKq9_-JI... 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 https://secure-web.cisco.com/1cd7RVInFeSE58D1bOWRT4VDultr79u7qyt1uj2QVJ3iqlJ... https://secure-web.cisco.com/1cd7RVInFeSE58D1bOWRT4VDultr79u7qyt1uj2QVJ3iqlJSi1cN5OnSxAkpJp1RnXMHNyZmhePtguHv8sLGygWWcnHjv_1XbaZF6py06rIKNUVJGnDgsQeqMJStg7ig_3q_CgRv_P6hzAxuN_xG8QsZ9AVgLH3SVNUNGskDlwfHFpdgGzQ3FKAmLB6gabtLBs8Tu-1M689W-jGbN_RunAhCOQyVqMnR6ECNI_3SaruofYL5dK75A0Ba9fojVbS4z-sb8GqjyZ92bhsWhaN33SIa7ueN5UZ0ZE03bBh2_rQybdnyiv2vONFvM0FUHJ_BC0wsBaDv823Qz1mLd8x7gXg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .