Bruce,
By "symlink from your /mnt/hgfs/mydata/fsaverage to /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s /mnt/hgfs/mydata/fsaverage /usr/local/freesurfer/subjects/fsaverage" ? which fsaverage is the target ?
Thanks, Mahmoud
The "target" fsaverage is the one that came with the installation. Which you no longer have so I have created a link for you to download it again and put it back in your $SUBJECTS_DIR (see next answer).
On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud zeydabadi@gmail.com wrote:
Bruce,
Thank you for your follow up and advice. Please let me know: 1- How to download the fsaverage again?
Ive created a link for you to download it: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz
2- should I do the symlink manually or it will be done by recon-all later ?
Just extract the file above into your $SUBJECTS_DIR so that you have a $SUBJECTS_DIR/fsaverage directory and recon-all will take care of the rest.
3- What steps should I take before running the recon-all -all ? should I create any specific directory? set any permission ?
None. Hopefully this will just work.
-Zeke