Dear All,
I am in the process of getting a powerful linux laptop to run Freesurfer.
Can I run Freesurfer on a 11.10 version of Ubuntu 64 bit ? Are there any
incompatibilities between the latest Freesurfer version and Ubuntu? Is
there any configuration issues and solution particular to my situation
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Hi Nick-
I was explicitly told by you there was not stable centos5 release of 5.1. And
unless it is located elsewhere, it is not located in:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/
Can you please clarify this?
Thanks,
Wil
|-Original Message-
|From: Nick Schmansky [
Apologies for the repost - this may have got lost in the mail blackout ...
Dear Freesurfer Experts,
I have read the advice on the wiki regarding what to do when pial surfaces
extend into the cerebellum. I had a few questions to clairfy things:
1) If I have made other (non-cerebellar) edits to t
Dear forum,
Has anyone else come across this issue and resolved it? If I try to switch the
main volume (after editing the vol), Tkmedit crashes with the following error
message:
% Bus error
It happens no matter what image I select and only when I try to load a new main
volume (not aux volume)
Laouchedi,
you will need to edit your recon-all script to correct a bug. find this
line:
if ($DoNuMakeUchar) set cmd = ($cmd --uchar transforms/talairach.xfm)
and replace it with this:
if ($DoNuMakeUchar) then
if ( ! -e transforms/talairach.xfm) then
echo "WARNING: transforms/talairach.xfm
Hi Dan,
Sure. It was in my earlier e-mail of today: I use tksurfer, see below. For this
last test, I used the SPM display function though, that now shows them to both
have the same orientation, so appears to be okay. Or am I still missing
something?
best,
Frank
Hi Dougla
Hi Frank,
I think we still need to know. What software are you using to view the volumes?
D
On Thu, Jan 19, 2012 at 10:59 AM, Léoné, F.T.M. (Frank)
wrote:
> Hi Doug,
>
> Ah, I found the cause myself, which might be useful for others. It happens
> already in the first step, before the ones I li
Hi Doug,
Ah, I found the cause myself, which might be useful for others. It happens
already in the first step, before the ones I listed: in mri_convert. I do:
mri_convert struct.nii 001.mgz
And it flips. This I can see because I converted the mgz back (mri_convert
001.mgz orig.nii) and then it
no, I think it's because the lh.curv is smoothed spatially
On Thu, 19 Jan
2012, Peter Savadjiev wrote:
> The reason I'm asking is because the mean of the principal curvatures thus
> obtained differs from the information stored in lh.curv, and I wasn't sure
> whether this is due to a different o
The reason I'm asking is because the mean of the principal curvatures
thus obtained differs from the information stored in lh.curv, and I
wasn't sure whether this is due to a different ordering of the vertices.
Best,
Peter
On 01/19/2012 10:51 AM, Peter Savadjiev wrote:
> Thanks Bruce,
>
> So I
My foray into custom-built binaries looks promising. Using the distributed
(CentOS4) build of 5.1, I'm running the Bert/Ernie benchmark in ~12 hours. If
I build this myself (using 4.1.2 / Red Hat 4.1.2-51) I can run in ~10 hours.
If I build the same code using the Intel compilers (12.0.0) wi
yes. All the surfaces for a given hemisphere share the same topology,
meaning vertex ordering, edges and faces.
On Thu, 19 Jan 2012, Peter
Savadjiev wrote:
> Thanks Bruce,
>
> So I can be sure that the output of the mris_command will be stored in the
> same order as lh.curv, and I can parcelate
Thanks Bruce,
So I can be sure that the output of the mris_command will be stored in
the same order as lh.curv, and I can parcelate it with lh.aparc.annot,
no matter which surface I use?
Best,
Peter
On 01/19/2012 10:46 AM, Bruce Fischl wrote:
> Hi Peter
> you can do it on any of the surfaces f
Hi Peter
you can do it on any of the surfaces for a given subject in the same
hemisphere.
cheers
Bruce
On Thu, 19 Jan 2012, Peter Savadjiev wrote:
> Hi,
>
> In order to obtain the vertices of lh.curv that belong to a specific
> freesurfer cortical ROI, such as 'superiortemporal', or
> 'superiorf
Hi,
In order to obtain the vertices of lh.curv that belong to a specific
freesurfer cortical ROI, such as 'superiortemporal', or
'superiorfrontal', etc., I use the information in lh.aparc.annot, as
described for example in
http://surfer.mnr.mgh.harvard.edu/fswiki/AnnotFiles/ .
However, now I
hi i have run freesurfer using -notalairach flag and i had the following
message :
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2
ERROR: cannot find transforms/talairach.xfm
can anyone know why is it searching the transforms/talairach.xfm when
I'm glad it worked out
Bruce
On Thu, 19 Jan 2012, LAOUCHEDI MAKHLOUF wrote:
hi everyone
i want just to inform you that it is ok with my problem of the
huge pathnames generated by our cluster
thank you very much
--- En date de : Sam 7.1.12, Nick Schmansky a
hi everyone
i want just to inform you that it is ok with my problem of the huge
pathnames generated by our cluster
thank you very much
--- En date de : Sam 7.1.12, Nick Schmansky a
écrit :
De: Nick Schmansky
Objet: Re: [Freesurfer] Fw : Re: get_4dfp_dim
Hi Thomas et al.,
I finally had luck with swapping over to XQuartz (2.7.0) - now the number
and depth of colors is back to normal.
cheers,
Fred
> Hi, was this problem ever resolved?
>
> I am seeing the same issue on my mac desktop.
>
> Thanks,
> Thomas
>
> On Mon, May 10, 2010 at 3:47 AM, Fred
Hi Douglas,
Ah, makes sense, sorry for that.
I do most of the work in SPM, so:
- I have a highres structural scan, nii file format
- I convert it to a surface using recon-all
- Coregister the highres structural to the functional scan, so it is
in the voxel size and orientation as the functional
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