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
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