Hi Martin,
thanks for your answer!
Editing and re-running the base (as a cross-sectional from after canorm)
improved the pial surface of the base, but did unfortunately not improve
the pial of the final output (.long.). Is it
possible/recommended to do the manual edits at other points in the
long
Hello Christophe, hello all,
I would like to know if the way that the transverse gyrus is labelled in
freesurfer, and specifically the fact that in the case of multiple
transverse gyri only the more anterior transverse temporal gyrus (ie;
Heschl's gyrus) is included, has changed across different
Hi Dana,
never seen this either. Have you tried rerunning the longitudinal of
that time point? Might be just a hickup. If it fails again at the same
location, we probably need the data. I think the base-data and the cross
sectional TP3 should be sufficient for us to replicate this.
Best, Martin
Hi Hakon,
have you checked the brainmask in the longitudinal run? It should be OK,
after fixing the base. If it looks OK, then the problems with the pial
surface must be due to something else.
You can do edits in the longitudinal run of that timepoint and re-run as
you would do in the standard (
Hello FreeSurfers,
I have inflated a couple surfaces less so that the gyri and sulci are more
prominent on the surface using the parameters:
mris_smooth -a 70 -n 70 -nw ./subj/surf/lh.white ./subj/surf/lh.smoothwm
mris_inflate -n 5 ./subj/surf/lh.smoothwm ./subj/surf/lh.inflated
mris_curvatu
Hi Tina,
We don't usually visualize them together, so translations are kind of
irrelevant for us. I don't have anything to translate them, but it would be
easy enough to do in matlab (or Amira I would think, although I haven't
used it)
sorry
Bruce
On Thu, 15 Oct 2009, Tina Jeon wrote:
> Hel
isxconcat-sess creates the files that you pass to mri_glmfit (ie,
multi-frame volumes and/or surfaces where each frame is a
subject). Something like:
AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii
You can then use this as input to mri_glmfit p
When I try to redo it, it does the exact same thing. And the same
thing is happening with a different subject as well.
At 06:43 PM 10/14/2009, Nick Schmansky wrote:
>What happens if you restart it? The log terminates in an odd place that
>I've never seen before.
>
>Nick
>
>On Wed, 2009-10-14 at
Thanks Doug,
I was just a bit confused because I thought the help for mri_glmfit
mentioned an osgm directory that wasn't there.
I was given a matlab script that does that now.
I'm using a command like this:
mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask
../tal.mask.nii
Th
What does your matlab script do? Your glmfit cmd looks fine.
On Thu, 15 Oct 2009, Maximilien Chaumon wrote:
> Thanks Doug,
> I was just a bit confused because I thought the help for mri_glmfit
> mentioned an osgm directory that wasn't there.
> I was given a matlab script that does that now.
>
From Christophe
Hi Narly
Hello Christophe, hello all,
I would like to know if the way that the transverse gyrus is labelled in
freesurfer, and specifically the fact that in the case of multiple
transverse gyri only the more anterior transverse temporal gyrus (ie;
Hi Nick,
After trying all of the steps below, the surfaces are much improved,
but the pial surface still has problems, particularly in the temporal
lobes (see below). So, maybe this is the best we can do with this
image. Thank you for helping out with this.
Thanks,
Dana
[]
At 06:58 PM 1
Hi Dana,
that is an impressively hard image. I think you'll need to do a fair
amount of manual editing to improve the segmentation (and remove
topological defects) in the temporal lobe.
Bruce
On Thu, 15 Oct 2009, Dana W.
Moore wrote:
> Hi Nick,
>
> After trying all of the steps below, the su
--
Christophe Destrieux
Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
37032 Tours - France
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
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We recently installed a Dell Blade server cluster running Freesurfer v4.5 under
CentOS 64-bit Linux, with each Blade server having two Intel Xeon E5405 quad
core CPUs, running at 2.0 GHz, 2x6144 KB cache and 16 GB of RAM, with a swap
file of size between 8-16 GB.
Using a single Blade server of
We are having the same issue after upgrade to FreeSurfer 4.5.
It takes more than 1.5 hrs for the jobs that used to complete in less
than 30 minutes.
Alex Zaitsev
Chris Hyatt wrote:
>
> We recently installed a Dell Blade server cluster running Freesurfer
> v4.5 under CentOS 64-bit Linux, with e
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