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

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

---

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