Thanks Bruce! So, I just move the SUBJECT_DIR folder and then setenv? I do want to set the subject directory to a new path Thanks again, Katica ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, September 03, 2013 12:03 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
setenv FREESURFER_HOME /usr/local/freesurfer On Tue, 3 Sep 2013, Boric, Katica A. wrote: > > > Hi everyone! > I wrote you last Friday regarding an error at the last moment of the MRI > processing (see e-mails below) > Zeke: thanks so much for the advice, I will move the SUBJECT_DIR to the same > folder system as $FREESURFER_HOME. > Could someone please show me how to set the directory with a tcsh shell? > The path to the freesurfer home is: usr/local/freesurfer > > Thank you very much, > Katica > > > ________________________________________ > From: Z K [zkauf...@nmr.mgh.harvard.edu] > Sent: Friday, August 30, 2013 12:41 PM > To: Boric, Katica A. > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error in MRI processing > > Katica, > > The file system in the physical computer is NTFS. But it looks like the > SUBJECTS_DIR is on a mounted filesystem. And your on a virtual machine. > Unfortunately there's lots of possibilities here for some type of > incompatibility with symbolic links. > > Would it be possible for you to set the SUBJECTS_DIR to be on the same > file system as $FREESURFER_HOME (locally) in order to avoid any > potential conflicts? > > -Zeke > > On 08/30/2013 11:54 AM, Boric, Katica A. wrote: >> Hi Doug! >> I am using free surfer on a VM. The file system in the physical computer is >> NTFS. >> Thanks, >> Katica >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Friday, August 30, 2013 11:46 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] error in MRI processing >> >> I think this error >> >> ln: failed to create symbolic link `./fsaverage': Operation not supported >> >> is a problem with your file system. Are you using a FAT file system? >> >> >> >> >> On 08/30/2013 11:41 AM, Boric, Katica A. wrote: >>> Hi Bruce this comes out from ls -ald $FREESURFER_HOME/subjects/fsaverage >>> >>> 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: >>> >>> >>> >>> >>> 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 >>> >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 _______________________________________________ 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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