i dont think the symlinks in the group analysis instance should be an issue either. the only time it would be is if the 'fsaverage' used to create the group analysis files (say, using recon-all -qcache) did not match the fsaverage found in your subjects dir, which would be the case if fsaverage was updated (which it hasnt in several years).
if you have the disk space, its always safer to just copy fsaverage to your subjects dir rather than use the symlink.
n.
On Wed, 2011-11-02 at 20:29 +0000, Vy Dinh wrote:
Thank you for the response Nick. Knowing that these are the only symlinks is reassuring. However, we do plan on running group analyses. The symbolic link within the subject directories already point to the local directory while my data are on the server (the folders were copied to the server after running recon-all).
I read through the Freesurfer tutorial for group analyses and it appears that the commands call fsaverage within SUBJECTS_DIR, not the links within each subjects directory, so perhaps the symbolic links may not be a concern for group analyses either?
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
From: Nick Schmansky [nicks@nmr.mgh.harvard.edu] Sent: Wednesday, November 02, 2011 3:13 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.goldman@gmail.com Subject: Re: [Freesurfer] concerns about symbolic links during processing
your solution of copying fsaverage and the EC_average dirs to your SUBJECTS_DIR is the proper one in this case. symlinks are used only to save space.
this data (fsaverage and EC_average) is used only during recon-all, and doesnt need to 'travel' with the subject data (unless you intend to recon-all later, or perform group analysis).
you should be able to move your subject data around without a problem (there are no other symlink except those two).
n.
On Wed, 2011-11-02 at 18:22 +0000, Vy Dinh wrote:
Dear experts,
We have recently encountered processing errors (during recon-all and -autorecon2&3) due to the creation of symbolic links within our SUBJECTS_DIR. Since our data were located on a data mount, the system somehow could not source the linked file. We have addressed this issue by directly copying fsaverage and th *EC_average files directly to our current SUBJECTS_DIR so that the symbolic links did not need to be created.
However, this brings to light some another concern. The subjects for our study were processed on a local computer and then copied to the server so that they could be processed on multiple computers. Since we wanted to keep a copy of the "raw" reconned data, we copied these subjects to another directory and proceeded to do manual edits. Are there other symbolic links created within the subjects directories or SUBJECTS_DIR that would become defunct with these copies? I read a post in the Freesurfer forum that the link to fsaverage (and other folders) were only created during recon-all for display purposes. However, when running group analyses, these folders/files will need to be accessed, so does that mean that we would have to change the path info in these links? Would you caution against moving the subject directories after recon-all has been run? Rather than all the steps in run recon-all again, are there specific functions that will recreate these links?
Thanks,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
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