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 [zkaufman@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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 [fischl@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
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