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Yes the symbolic link did exist, but the fsaverage directory was empty. I downloaded and reinstalled FreeSurfer again and everything seems to be working fine. I’m not sure why my version of FreeSurfer was missing everything inside the fsaverage directory. 

Naomi

On May 20, 2018, at 1:13 PM, Antonin Skoch <ansk@ikem.cz> wrote:

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Hi Naomi,

does the symbolic link


exist in your filesystem?

Antonin Skoch


Hello FreeSurfer Developers, 

I'm attempting to run FreeSurfer but I get the following error when I run the recon-all command: 

> ERROR reading /panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage/label/lh.BA1_exvivo.label <http://pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage/label/lh.BA1_exvivo.label>; 

I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
2) Platform: Red Hat Enterprise Linux Server release 6.6 (Santiago) 
3) uname -a: Linux m8-8-5 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux 
4) recon-all.log: see attached 

Thanks, 

Naomi 
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