This comes out: drwxrwxrwx. 1 root root 0 Aug 29 11:10 /mnt/hgfs/Linux_Share/subjects ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 11:11 AM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
that probably means you don't have write access to the subject directory. Can you run: ls -ald /mnt/hgfs/Linux_Share/subjects On Fri, 30 Aug 2013, Boric, Katica A. wrote: > It says: > $ ln -s /usr/local/freesurfer/subjects/fsaverage > ln: failed to create symbolic link `./fsaverage': Operation not supported > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, August 30, 2013 11:04 AM > To: Boric, Katica A. > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error in MRI processing > > can you run: > > cd /mnt/hgfs/Linux_Share/subjects > ln -s /usr/local/freesurfer/subjects/fsaverage > > and tell us what it says? > Bruce > On Fri, 30 Aug 2013, Boric, > Katica A. > wrote: > > > 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 > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
