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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:

    External Email - Use Caution        

Hi Naomi,

does the symbolic link

/panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage

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 http://pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage/label/lh.BA1_exvivo.label%3E;

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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