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.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.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