On Wed, Sep 17, 2014 at 10:21 AM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

No it doesnt make a difference.

Are you using a the virtual machine version of freesurfer with a shared
folder? Or some other system where you are mounting a readonly file
system? That is most likely your issue.

You will have to place your subjects directory onto a location in which
you have write permissions.

-Zeke

On 09/17/2014 10:16 AM, Mahmoud wrote:
> Paul,
>
> I am using bash instead of tcsh. Does it make any difference ?
>
> Mahmoud
>
> On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com
> <mailto:pabeach1@gmail.com>> wrote:
>
> Hmm. Well I'm stumped. Sorry. :-/
>
> Any Freesurfer gurus have some ideas here?
>
> On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com
> <mailto:zeydabadi@gmail.com>> wrote:
>
> Paul
>
> it shows again:
> ln: failed to create symbolic link ‘./fsaverage’: Operation not
> supported
>
> !!!
>
> On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach <pabeach1@gmail.com
> <mailto:pabeach1@gmail.com>> wrote:
>
> you have to tell the symbolic link where to put the directory
>
> copy this exactly into your terminal, including the period
> at the end
>
> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
> cd $SUBJECTS_DIR
> ln -s $FREESURFER_HOME/subjects/fsaverage .
>
>
>
> On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud
> <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>> wrote:
>
> Paul,
>
> I tried this:
> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
> cd $SUBJECTS_DIR
> ln -s $FREESURFER_HOME/subjects/fsaverage
>
> and got this:
> ln: failed to create symbolic link ‘./fsaverage’:
> Operation not supported
>
> any idea ?
>
> Mahmoud
>
> On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach
> <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote:
>
> Try something like:
>
> cd $SUBJECTS_DIR
> ln -s $FREESURFER_HOME/subjects/fsaverage .
>
> Confirm the linked directory is now in your
> $SUBJECTS_DIR, then try running your script.
>
> On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud
> <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>
> wrote:
>
> Paul,
>
> The fsaverages are in $FREESURFER_HOME/subjects.
> So does it mean that the program couldn't make a
> link between my actual image places and
> $FREESURFER_HOME/subjects/fsaverage ?
> what can I do to fix it ?
>
> Thank you,
> Mahmoud
>
> On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach
> <pabeach1@gmail.com <mailto:pabeach1@gmail.com>>
> wrote:
>
> The general fsaverage (as well as it's other
> iterations, fsaverages 3-6) should be
> located in your $FREESURFER_HOME/subjects
> directory. You could symbolically link it
> over to your $SUBJECTS_DIR.
>
> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud
> <zeydabadi@gmail.com
> <mailto:zeydabadi@gmail.com>> wrote:
>
> Dear All,
>
> I ran the following script:
>
> #!/bin/bash
> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
> recon-all -i
> /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
> -subject case022_tp2 -all
>
> and got the error below at the end.
> Could anybody please let me know how to
> fix it.
>
> Thank you,
> Mahmoud
>
>
> Reporting on 70 segmentations
> mri_segstats done
> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
> #--------------------------------------------
> #@# BA Labels lh Tue Sep 16 19:26:47 PDT
> 2014
> INFO: *fsaverage subject does not exist
> in SUBJECTS_DIR*
> INFO: Creating symlink to fsaverage
> subject...
>
> cd /mnt/hgfs/DBSI/volumetric/MGZ; 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/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
> --trgsubject case022_tp2 --trglabel
> ./lh.BA1.label --hemi lh --regmethod
> surface
>
> No such file or directory
> mri_label2label: could not open label
> file
> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
>
> srclabel =
> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
> srcsubject = fsaverage
> trgsubject = case022_tp2
> 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/DBSI/volumetric/MGZ
> FREESURFER_HOME /usr/local/freesurfer
> Loading source label.
> Invalid argument
> ERROR reading
> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
> Linux ubuntu 3.13.0-35-generic
> #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC
> 2014 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s case022_tp2 exited with
> ERRORS at Tue Sep 16 19:26:47 PDT 2014
>
> For more details, see the log file
> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
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> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU *Co*gnitive and *Ge*riatric *N*eurology
> *T*eam (*CoGeNT*)
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> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam
> (*CoGeNT*)
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>
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> Compliance HelpLine at
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> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
>
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>
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