That could be the case. I start recon-all and just leave the computer for 24 hrs. Is there a way to find out what could be doing this.Anil.On 7/17/06,
Bruce Fischl <[EMAIL PROTECTED]> wrote:
is there some builtin time limit that you are exceeding? The log file justsays:mri_remove_neck -radius 25 n
Hi Akram,
I'm working on the huge ventricle problem. We are also getting ready to
release a version that should fix the crossing-the-midline problem, if
that's what you're experiencing.
Bruce
On Mon, 17 Jul 2006, Akram Bakkour wrote:
Hi all,
I've been having trouble with these two brains
One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set
them to 1 in the output. In this case, it will make a binary mask of the
left cerebral white matter as that has a cod
It depends on how you get your images in the first place. If you use
mri_convert to convert from dicom files, then it uses information in the
dicom header. I'm attaching the rules that mri_convert uses. If you get
your data from somewhere else, then mri_convert will try to find the
orientatio
When reporting a bug or a problem, you should follow the instructions in
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
thanks
doug
Jake Freimer wrote:
I have run several instances of autorecon2 and have only got left
hemisphere data. The log file says that autorecon finished with errors
Hello everyone,
orientation i guess is quite an issue.
Well how does,Freesurfer determine orientation of the
image.Do I have to know how the image has been
processed before it reaches me or is there any other
way to find out?Does it have to do with the 'flip'?
I checked the orientation of an imag
Hi all,
I've been having trouble with these two brains with huge ventricles, first the
aseg failed, and the ventricles didn't get filled automatically, so I filled
them manually and ran recon-all -autorecon2-wm but my surfaces were off and
there was a blatant hemispheric devision problem with
What is the error message when it crashes? How much memory does each
node have? It should have at least 2GB.
On Mon, 2006-07-17 at 11:20 -1000, Renat Yakupov wrote:
> Hello everybody,
>
>
>
> Does anybody run FreeSurfer on Linux clusters in general or Scyld
> BeoWulf clusters in particular?
Can you send the recon-all.log file? I can examine it for error
messages.
Also, do the input files contain orientation info? run this on your
subject input volume:
mri_info 001.mgz
and send me the output.
On Mon, 2006-07-17 at 13:58 -0700, Jake Freimer wrote:
> I have run several instances
Hello everybody,
Does anybody run FreeSurfer on Linux clusters in general or
Scyld BeoWulf clusters in particular? Do you have any problems?
We are having some problems running FreeSurfer on our
cluster. Quite often when we run autorecon2 stage on a compute node, it
crashes. Sometimes
Dear all,
Does aseg save out masks of the various subcortical regions measured?
If so, is it possible to visualize and/or edit these in tkmedit/scuba,
or export them to an external format?
Thanks,
Sasha
Disclaimer:
The materials in this e-mail are private and may contain Protected Health
Inf
I have run several instances of autorecon2 and have only got left
hemisphere data. The log file says that autorecon finished with errors
but I can not find where to find these errors. I believe that the
problem is the way the data being fed in is oriented so I was
wondering how I should reorient i
A further clarification. This has to do with the server end of things, not
the viewer end.
Satra
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Satrajit Ghosh
Sent: Monday, July 17, 2006 1:36 PM
To: 'Joe Berens'; freesurfer@nmr.mgh.harvard.edu
Subject:
Hi Joe,
You may want to try realvnc (www.realvnc.com). We have been trying their
enterprise edition and it works really well. The typical vnc server that's
installed does not support OpenGL. I do know that more recent editions of
realvnc do support the GLX extension.
Cheers,
Satra
-Origina
Joe,
Does tkmedit work directly on the RH3 box? If so, then it is the windows
box that does not have the GLX extensions built into its OpenGL driver.
GLX allows running X windows apps (like tkmedit) to run using the OpenGL
calls locally on a machine (for performance). I don't have experience
ru
Hello,
A user gets the following:
GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by
display: :60.0
This is using tightvnc via ssh from a windows xp box to Redhat Enterprise 3.
Every thing else seems to work fine. Any Ideas?
-Joe
A
Hi Isabel,
if dura is left around you are *much* better off than if brain is stripped.
In the latter case we will never recover, while if there is some dura we
generally can avoid including it in the surfaces. Note that in the
screenshots you attached that the dura was labeled as cortex by the
17 matches
Mail list logo
