Hello Freesurfer experts,
I am having a tough time getting my pial surfaces into the correct
anatomical space. I work with ECoG Patients, so we have pre-implant high
resolution T1s (GE SPGR), and post-implant high resolution CTs that show
the location of ECoG electrodes within the patient's skull.
Yes, that should be fine
On 09/16/2014 09:50 PM, prasser wrote:
> Say, following the set of commands given on the FsTutorial/Diffusion
> page (freesurfer.net/fswiki/FsTutorial/Diffusion)
>
> On Mon, 15 Sep 2014 05:26:01 -0700 *Bruce Fischl
> * wrote
>
> what kind of DTI analysis?
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
Dear Freesurfer users,
I have used the command bb_register to automatically register raw fMRI data on
the anatomy. The output looks visually fine, however the mincost file gives me
values around 0.5 for my subjects. Is this range acceptable? Does anybody has a
hint on how the registration could
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
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
Repo
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