Hi Bruce! Thanks for your fast response. /usr/local/freesurfer/subjects/fsaverage does exists!
Thanks again, Katica ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 10:51 AM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing Hi Katica does /usr/local/freesurfer/subjects/fsaverage exist? Do you have write access to /mnt/hgfs/Linux_Share/subjects? cheers Bruce On Fri, 30 Aug 2013, Boric, Katica A. wrote: > Hi everyone! > I am new to freesurfer, and I was processing and MRI using "recon-all > -autorecon1 -autorecon2 -autorecon3" command and I have a message that the > processing was exited with ERRORS. When checking the recon-all. log it > appears that these are the error (highlighted in yellow): > > #@# BA Labels lh Thu Aug 29 22:14:42 PDT 2013 > INFO: fsaverage subject does not exist in SUBJECTS_DIR > INFO: Creating symlink to fsaverage subject... > > cd /mnt/hgfs/Linux_Share/subjects; ln -s > /usr/local/freesurfer/subjects/fsaverage; cd - > > ln: failed to create symbolic link `./fsaverage': Operation not supported > > mri_label2label --srcsubject fsaverage --srclabel > /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label --trgsubject > MGH013_SurferOutput --trglabel ./lh.BA1.label --hemi lh --regmethod surface > > No such file or directory > mri_label2label: could not open label file > /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label > > srclabel = /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label > srcsubject = fsaverage > trgsubject = MGH013_SurferOutput > trglabel = ./lh.BA1.label > regmethod = surface > > srchemi = lh > trghemi = lh > trgsurface = white > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /mnt/hgfs/Linux_Share/subjects > FREESURFER_HOME /usr/local/freesurfer > Loading source label. > Invalid argument > ERROR reading /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s MGH013_SurferOutput exited with ERRORS at Thu Aug 29 22:14:43 > PDT 2013 > > If any of you could give us any advice on how to fix this we would really > appreciate it! > Thank you very much, > > Cheers, > Katica > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
