On Wed, Sep 17, 2014 at 11:05 AM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

I dont know all the details regarding shared directories between the
host and guest, but the bottom line is that if you can not manually
create a symbolic link in the subjects dir than you will not be able to
run recon-all.

Another option is to use the shared directory to copy the subjects dir
into the file system in virtual machine space.

-Zeke

On 09/17/2014 10:33 AM, Mahmoud wrote:
> Zeke,
>
> I'm running Ubuntu 14.04 as guest on a VMware® Workstation 10 and
> Windows 7-64 as host.
> I made a shared directory between windows and Ubuntu named DBSI where
> then I put the /volumetric/MGZ under it.
> So, how can I give permission for that ?
>
> Mahmoud
>
> On Wed, Sep 17, 2014 at 10:21 AM, Z K <zkaufman@nmr.mgh.harvard.edu
> <mailto: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>
> > <mailto: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>
> > <mailto: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>
> > <mailto: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>
> <mailto: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>
> <mailto: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> <mailto: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> <mailto: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>

> > <mailto: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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> >

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> >
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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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> >
> > --
> > 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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> > sender and properly
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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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