Thank you Bruce
On Thu, Jun 22, 2017 at 12:45 AM, Bruce Fischl
wrote:
> sounds like more in the graphics card, or just reduce the number of
> simultaneous jobs
>
> On Wed, 21 Jun 2017, Ramesh Babu wrote:
>
> Dear Douglas Greve and Bruce,
>>
>> Thanks for your reply. I am using 16GB RAM and 2 GB
Hi Gabor,
I'm not sure it is identical, but it should be pretty close
cheers
Bruce
On Wed, 21 Jun
2017, Gabor Perlaki wrote:
Dear all,
Could anybody help me with the below questions please?
Dear all,
I've found an article comparing DK and DKT atlas based automatic
segmentations to
Hello Maria,
This is a known issue with a freesurfer v6 script and more recent
versions of macOS. Can you please source freesurfer and then issue the
following command:
sudo -E fs_update
Its should update your installation and resolve the issue.
On 06/21/2017 11:43 AM, Maria Economou wr
Can you send me your recon-all script to my email address (not to the
list). I suspect it has been modified.
On 06/21/2017 02:04 PM, Michael Davies wrote:
> Hello, i have been trying to regenerate the surface on one of my
> subjects but keep having a problem where the terminal is saying there is
Dear all,
Could anybody help me with the below questions please?
Dear all,
>
>
> I've found an article comparing DK and DKT atlas based automatic
> segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012;
> 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/). It seems
sounds like more in the graphics card, or just reduce the number of
simultaneous jobs
On Wed, 21 Jun 2017, Ramesh Babu wrote:
Dear Douglas Greve and Bruce,
Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should I
increase memory of both or only graphic card?
Thanks
Ramesh
Hi Maria – Can you please run the mri_info command on the same nifti volume on
the same computer and let us know what the output is?
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Maria Economou
mailto:meconom...@sheffield.ac.uk>>
Reply-To: Freesurfer support list
mai
Hello, i have been trying to regenerate the surface on one of my subjects but
keep having a problem where the terminal is saying there is a missing file
name. Do you have any suggestions please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-centos6_x86_64
Hi Marine
the brainmask is just a rough estimate of what is brain and what is not.
You don't need to worry if it is not accurate *unless* the lh.pial and/or
rh.pial surfaces end up not being accurate because of dura left in the
brainmask.
cheers
Bruce
On Wed, 21 Jun 2017, Lisa Delalande wrot
Hi Mariana
yes, control points would mess everything up. It looks like the rest of the
surface was generated pretty accurately though - do you need to correct
anything?
cheers
Bruce
On Wed, 21 Jun 2017, Budge,
Mariana wrote:
Hi Freesurfer experts,
I am running FS on a patient with a
Hi,
I am a PhD student and faced a problem with Freesurfer, more specially with
segmentation. First of all, I did a typical qsub command. However, when I
cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are
often considered as grey matter.
I tried these different commands :
Thanks Doug! It works!
Best Wishes,
Elijah
On 21 June 2017 at 16:09:29, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:
use this script
https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table
On 06/21/2017 10:53 AM, Elijah Mak wrote:
> Hi Freesurfer Team
>
> Apologies fo
Dear Freesurfer community,
I'm having trouble completing the pre-processing step for TRACULA analysis.
I'm using a single NifTi file which I've converted using the original
DICOMS, acquired by a PHILIPS scanner. However, I get the following errors
in the command line:
dyld: lazy symbol binding f
use this script
https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table
On 06/21/2017 10:53 AM, Elijah Mak wrote:
> Hi Freesurfer Team
>
> Apologies for bumping this thread up again. I am wondering if is there
> is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc
> (us
Hi Freesurfer Team
Apologies for bumping this thread up again. I am wondering if is there is a way
to extract the ROI stats in gtm.stats.dat after mri_gtmpvc (using a similar
approach such as asegstats2table)?
Thanks for your help!
Best Wishes,
Elijah
On 16 June 2017 at 16:53:33, Elijah Mak
Dear Doug,
Thanks a lot for your help, it worked as expected.
Best,
Ismail
2017-06-20 16:31 GMT+02:00 Douglas Greve :
> Can you use annotval2surfoverlay.m ? it can be found in
> $FREESURFER_HOME/matlab or here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
>
> On 6
Hello, i have been trying to regenerate the surface on one of my subjects but
keep having a problem where the terminal is saying there is a missing file
name. Do you have any suggestions please?
Kind regards, Michael
bash-4.1$ freesurfer_setup_freeview
freesurfer-Linux-centos6_x86_64
Dear Douglas Greve and Bruce,
Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should I
increase memory of both or only graphic card?
Thanks
Ramesh
On Tue, Jun 20, 2017 at 9:02 PM, Bruce Fischl
wrote:
> or don't run so many at the same time
>
> cheers
> Bruce
> On Tue, 20 Jun
Hi,
I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8
mm, population 1, population 2 , and age as nuisance factor.
After POS MC simulation CW correction, I had two significant clusters resulting
from this in the planum temporale and Heschl’s sulcus. The contrast bei
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