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
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 wro
Yeah, I was starting to wonder if he was having permissions issues as well.
On Wed, Sep 17, 2014 at 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 wrote:
>
>> Hmm. Well I'm stumped.
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 w
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 wrote:
> Hmm. Well I'm stumped. Sorry. :-/
>
> Any Freesurfer gurus have some ideas here?
>
> On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud wrote:
>
>> Paul
>>
>> it shows agai
Hmm. Well I'm stumped. Sorry. :-/
Any Freesurfer gurus have some ideas here?
On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud 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 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 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
>
> SU
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 wrote:
> Paul,
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 wrote:
> Try someth
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 wrote:
> Paul,
>
> The fsaverages are in $FREESURFER_HOME/subjects. So does it mean
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 wrote:
> The general fs
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 wrote:
> Dear All,
>
> I ran the following script:
>
> #!/bi
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