Open position: PhD in multimodal imaging of the vulnerability to develop
schizophrenia
OFFICE MEDICO-PEDAGOGIQUE, Laboratoire de neurosciences et neuroimagerie en
psychiatrie de l’enfant et de l’adolescent
Starting date: October 1st 2015
Working environment: In the context of a longitudinal stud
Hi list,
I 'm continuing to have problem to run mni305 volume-based analysis.I have read
the guide
(http://freesurfer.net/fswiki/FsFastFunctionalConnectivityWalkthrough?highlight=%28mkanalysis%5C-sess%29%7C%28connectivity%29).It
explains that separate mkanalysis-sess commands will need to be ru
Hi Daniel
I believe that:
setenv OMP_NUM_THREADS 1
should do the trick, although I'm not positive what version is run in the
HCP pipeline. See if this env variable is set in the recon-all script.
cheers
Bruce
On Wed, 3 Jun 2015, Daniel P. Bliss wrote:
Hi all,
I'm running the FreeSurferPi
Hi Jen
look at the references in that paper to Kennedy/Caviness and such. The
auto labeling is based on the manual protocol developed by the Center
for Morphometric Analysis at MGH and is published in a number of papers.
cheers
Bruce
On
Thu, 4 Jun 2015, Jennifer Eastman wrote:
> Hello,
>
> I
Hi Ashkan
the mapping is nonlinear so can't be represented by a matrix. Because it's
(highly) nonlinear, under it most subjects look a lot like each other, so
adding subjects to fsaverage doesn't usually change it. That said, try out
make_average_subject and see what it produces if you want an
Hi Daniel,
maybe also try recon-all -openmp 1 ?
Martin
On 06/04/2015 08:22 AM, Bruce Fischl wrote:
Hi Daniel
I believe that:
setenv OMP_NUM_THREADS 1
should do the trick, although I'm not positive what version is run in
the HCP pipeline. See if this env variable is set in the recon-al
Daniel,
The recon-all script sets OMP_NUM_THREADS to 1 at the start of the script, and
is changed only if the -openmp flag is used. its very strange that you
are seeing em_reg set to 40. in your recon-all.log, search for ‘openmp’, and
it should show ‘1’ by default. you could also add -debug
The mkanalysis-sess command should be almost identical for all 3
analyses. The only thing you would change is "-surf fsaverage lh" "-surf
fsaverage rh" or "-mni305"
doug
On 06/04/2015 03:21 AM, std...@virgilio.it wrote:
>
> Hi list,
>
>
> I 'm continuing to have problem to run mni305 volume-bas
I'm sorry Doug but I should run mkanalysis-sess -mni305 for both right and left
thalamus (which are taskreg).
Specifically, I'm performing
mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh -fwhm 5
-notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5
-polyfi
Yep, in my recon-all script, OMP_NUM_THREADS is set to 1. But I should be
clear here that the call to mri_em_register that is using 40 threads is
being made directly in the FreeSurferPipeline script -- i.e., *not* inside
recon-all. Does that change anything?
Many thanks for the help,
Dan
On Thu
yes, that certainly changes things. You'll need to modify that script and
set it to 1
On Thu, 4 Jun 2015, Daniel P. Bliss wrote:
Yep, in my recon-all script, OMP_NUM_THREADS is set to 1. But I should be
clear here that the call to mri_em_register that is using 40 threads is
being made directly
As you prepare your posters for the OHBM conference, please remember to
acknowledge and/or cite FreeSurfer on posters where you have used
FreeSurfer tools. You could also consider including the FreeSurfer logo
(attached) on your poster.
thanks and see you in Hawaii!
The FreeSurfer Team
PS:
On 06/04/2015 11:55 AM, std...@virgilio.it wrote:
> I'm sorry Doug but I should run mkanalysis-sess -mni305 for both right
> and left thalamus (which are taskreg).
>
> Specifically, I'm performing
>
> mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh
> -fwhm 5 -notask -taskre
Yep, that did the job for me. Many thanks!
-- Dan
On Thu, Jun 4, 2015 at 9:19 AM, Bruce Fischl
wrote:
> yes, that certainly changes things. You'll need to modify that script and
> set it to 1
>
> On Thu, 4 Jun 2015, Daniel P. Bliss wrote:
>
> Yep, in my recon-all script, OMP_NUM_THREADS is se
14 matches
Mail list logo
