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_d...@rush.edu > > ________________________________________ > From: Douglas N Greve [gr...@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_d...@rush.edu >> >> ________________________________________ >> From: Douglas N Greve [gr...@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_d...@rush.edu >>> >>> ________________________________________ >>> From: Douglas N Greve [gr...@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_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. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> -- >>> 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 >>> >>> >>> _______________________________________________ >>> 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 >> >> >> >> >> > > -- > 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 > > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
