this: drwxr-xr-x. 7 root root 4096 Oct 23 2012 /usr/local/freesurfer/subjects/fsaverage ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 11:15 AM To: Boric, Katica A. Subject: Re: [Freesurfer] error in MRI processing
how about: ls -ald $FREESURFER_HOME/subjects/fsaverage On Fri, 30 Aug 2013, Boric, Katica A. wrote: > 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 > > > _______________________________________________ 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. 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