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_d...@rush.edu ________________________________________ From: Douglas N Greve [gr...@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_d...@rush.edu <mailto:vy_d...@rush.edu> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
