The BA labels should be in
$FREESURFER_HOME/subjects/fsaverage/label
doug Vy Dinh wrote:
5.0
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: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, October 21, 2011 9:51 AM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3
So the BA labels don't exist in $FREESURFER_HOME/subjects/fsaverage/label? What version are you using? doug
Vy Dinh wrote:
You're absolutely right. The lh.BA1.label file is missing within freesurfer/fsaverage. I thought that we may have had the same issue as this poster (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19399.html) since we use a mount, but it seems that the missing BA labels is the real issue. My main concern, then, is how this has affected our processing (besides not running the BA labels) and whether any reruns would be necessary. In other words, did recon-all simply skip the BA labels and ran the other processes or did it crash midway?
Also, if you have uploaded a fsaverage folder that contains these missing files, I will gladly download them from your site. Note that we had run the recon-all commands with Freesurfer version 5.0. This error was never encountered until recently (even though we had not upgraded to the newer version).
Thank you for your time,
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: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, October 20, 2011 1:10 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3
No, it means that it cannot find that file. doug
Vy Dinh wrote:
Then does it mean that I can ignore this error message?
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: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, October 20, 2011 12:51 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3
It does need to be there, but usually it creates it's own symbolic link (so you should not need to copy it). doug
Vy Dinh wrote:
Hi Douglas,
Thank you for your reply. The subdir is just an example, so that is probably a typo in the original post. Fsaverage/ did not exist in SUBJECTS_DIR when we ran the recon commands, so in response to the error, I copied fsaverage/ from the freesurfer directory to my SUBJECTS_DIR. I guess my concern now is whether we need to run the autorecon-all and any subsequent -autorecon processes (with the fsaverage/ folder in SUBJECTS_DIR).
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: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, October 20, 2011 12:26 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3
Does /Users/subdir/ fsaverage exist? Also, it looks like there could be a space between "subdir/" and "fsaverage" doug
Vy Dinh wrote:
Dear Experts,
I ran the wm.mgz corrections and pial corrections using the command:
-autorecon2 –autorecon3 –subjid sub2
However, Freesurfer exited the program with the following message:
SUBJECTS_DIR /Users/subdir FREESURFER_HOME Applications/freesurfer Loading source label. No such file or directory fsaverage/label/lh.BA1.label ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label Darwin mso00820bg.rush.edu http://mso00820bg.rush.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
Can someone please explain what this error message means regarding whether I need to rerun the autorecon processes with the fsaverage folder within my current subjects folder? I copied fsaverage/ from freesurfer/ to my designated SUBJECTS_DIR but have not run the recon. It seems that the pial surfaces were regenerated while the white matter segment was not corrected for this one subject. I ran other subjects within this SUBJECTS_DIR (before I copied the fsaverage folder) but the white matter segment and pial surfaces were regenerated for them. Looking forward to your responses.
Thank you,
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 mailto:Vy_dinh@rush.edu
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html