Freesurfer distributes ‘fsaverage’ under $FREESURFER_HOME/subjects directory. recon-all should create symbolic link to $FREESURFER_HOME/subjects/fsaverage under $SUBJECTS_DIR.

This is from your recon-all.log “ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/Freesurfer “

You are setting SUBJECTS_DIR to your Freesurfer install directory. It is a good idea to set SUBJECTS_DIR to some other directory that you have write permission.

Your recon-all failed because of “Too many levels of symbolic links”. Can you check what you have under $FREESURFER_HOME/subjects?

ls -l $FREESURFER_HOME/subjects

You should have these in the directory: drwxrwsr-x. 2 zkaufman fsbuild 4096 Mar 13 2012 cvs_avg35 drwxrwsr-x. 2 zkaufman fsbuild 4096 Apr 14 2015 cvs_avg35_inMNI152 dr-xr-sr-x. 2 ah221 fsbuild 4096 Mar 8 2023 fsaverage drwxrwsr-x. 2 zkaufman fsbuild 4096 Sep 22 2009 fsaverage3 drwxrwsr-x. 2 zkaufman fsbuild 4096 Sep 22 2009 fsaverage4 drwxrwsr-x. 2 zkaufman fsbuild 4096 May 31 2011 fsaverage5 drwxrwsr-x. 2 zkaufman fsbuild 4096 Sep 22 2009 fsaverage6 drwxrwsr-x. 2 zkaufman fsbuild 4096 Apr 12 2018 fsaverage_sym drwxrwsr-x. 2 zkaufman fsbuild 4096 Mar 30 2010 lh.EC_average -rw-rw-r--. 1 zkaufman fsbuild 1512 Dec 29 2016 README drwxrwsr-x. 2 zkaufman fsbuild 4096 Mar 30 2010 rh.EC_average -rw-rw-r--. 1 zkaufman fsbuild 6280209 Dec 29 2016 sample-001.mgz -rw-rw-r--. 1 zkaufman fsbuild 6269785 Dec 29 2016 sample-002.mgz drwxrwsr-x. 2 zkaufman fsbuild 4096 Nov 11 2008 V1_average

Your recon-all should have created this link ‘fsaverage -> /usr/local/freesurfer/subjects/fsaverage’ in the directory as well. Remove link. Set SUBJECTS_DIR to some other directory and restart recon-all.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Suman Saha Sent: Monday, November 27, 2023 11:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fwd: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to run recon-all command, but I get the following error when I run the "recon-all -i sub.mgz -s sub1 -all" command:

ERROR:

ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023

Does anyone have any thoughts on how to trouble-shoot this one? I've attached the recon-all.log.

1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu 22.04.1

3) recon-all.log: see attached

4) recon-all.error : see attached

---------- Forwarded message --------- From: Suman Saha <ecesuman06@gmail.commailto:ecesuman06@gmail.com> Date: Sat, Nov 25, 2023 at 8:17 AM Subject: ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label To: <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>

Hello FreeSurfer Developers,

I'm attempting to run recon-all command, but I get the following error when I run the "recon-all -i sub.mgz -s sub1 -all" command:

ERROR:

ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label Linux cbdl 6.2.0-37-generic #38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s my_sub exited with ERRORS at Fri Nov 24 23:43:39 IST 2023

Does anyone have any thoughts on how to trouble-shoot this one? I've attached the recon-all.log.

1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu 22.04.1

3) recon-all.log: see attached

4) recon-all.error : see attached