Martin,
Do you have a Mac intel or PowerPC?
I am using Mac Intel, with Matlab 7.3 (release 2007a) and don't get
this problem. Just to try, I relaunched the code with Matlab 7.4
(2007b), and got the same problem that you have, so that it should be
related to a specificity of the Matlab 7.4
Hi,
I am using freesurfer v4.0.2 on Mac OS Tiger and am getting a qdec error
message: WARNING: Marker for class Main was invalid
And
ERROR: In
/usr/pubsw/packages/KWWidgets/CVS/src/KWW., line 1182
VtkKWQdecApp : TclTkerror:
Invalid command ... "vtkTemp249"
I have substituted to old vers
How much detail do you need frmo the mgh file? I wrote a quick Python
script which reads in at least the volume data but I think I just passed
over most of the other stuff in there...
Yaroslav Halchenko wrote:
Does anyone know any handy module to at least read in .mgh files from
Python? Or sho
We are currently attempting to check the FA registration of each subject within
an MS study group using the following command:
tkregister2 --s fsaverage --surf white --reg
/Volumes/Data/magnims/group_study/P??-??/dti_analysis/fa-tal.nii.reg --mov
/Volumes/Data/magnims/group_study/P??-??/dti_ana
actually I need thickness data out of it. Is .mgh format documented
somewhere?
On Thu, 24 Apr 2008, Pádraig Kitterick wrote:
> How much detail do you need frmo the mgh file? I wrote a quick Python
> script which reads in at least the volume data but I think I just passed
> over most of the ot
Here you go Yaroslav...
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
Krish
On Apr 24, 2008, at 11:49 AM, Yaroslav Halchenko wrote:
actually I need thickness data out of it. Is .mgh format documented
somewhere?
On Thu, 24 Apr 2008, Pádraig Kitterick wrote:
How much detail d
You'll see we have a few Qs!
We have been having problems with a couple datasets with patients who have
severe atrophy (MS and Alzheimer's) where they fail in autorecon1 with the
Talairach QA check. The registrations look fine so I was wondering what other
problems might cause this check to fai
In addition to this we have several datasets here that have a couple of
subjects failing with:
Killed
ERROR: mri_ca_register with non-zero status
Linux jalapeno14 2.6.20-1.2320.fc5 #1 SMP Tue Jun 12 18:50:49 EDT 2007 x86_64
x86_64 x86_64 GNU/Linux
I see from the new 4.0.3 release notes that the
Yaroslav,
The mgh format is pseudo-documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
But the thickness data is not stored in mgh format, but rather in
another proprietary format, with documentation here:
http://wideman-one.com/gw/brain/fs/surfacefileformats.htm
Yo
Damian,
The talairach check can be bypassed with the -notal-check flag added to
recon-all.
Nick
On Thu, 2008-04-24 at 17:02 +0100, Damian Jenkins wrote:
> You'll see we have a few Qs!
>
> We have been having problems with a couple datasets with patients who have
> severe atrophy (MS and Alzhe
MGH is just a generic volume-based format so I think thickness data will
be stored in a 1xNumVerticesx1x1 volume. Here is a python function which
reads in the volume data. It's basically a translation of the readmgh
function from the Freesurfer matlab toolbox. You can modify it to return
more p
Damian,
Yes, it would be worth the effort to try v4.0.3 to see if the problem is
corrected. While the problem with mri_ca_register seemed to manifest
itself only on Darwin, the source of that bug was not Darwin specific,
so in theory it could appear on Linux (but we had never actually
encountered
Hello,
I need to determine the transform between the surface coordinates
between FS and the surface generated using some of the tools from JHU.
I think that I have a handle on this, but just wanted to confirm a
couple things.
1) First, the "voxel to ras transform" returned by 'mri_info' is the
tr
Pádraig is correct in stating that thickness data can be stored in an
mgh file. But the default output of the freesurer recon-all stream does
not store them in that format: it will output ?h.thickness files, which
are the proprietary format.
However, those can be converted to .mgh like this:
mri
Christine,
The warning message can be ignored.
As for the error, can you try v4.0.3? I have heard of the problem you
are seeing but have never been able to recreate it locally. I suspect
it might be rooted in the KWWidgets library, which is distributed with
freesurfer, and was updated from v4.0
Martin and other -localGI users,
Independent of the matlab problem, there was a bug that was just
discovered, affecting mris_fill, that breaks the -localGI usage. A fix
will be provided (hopefully along with a fix for this matlab problem) in
v4.0.4. If you need to use the -localGI feature, I can
Hi all,
We are having a problem running tksurfer on several Centos 5 machines.
We are getting the dreaded GLXBadLargeRequest and just the front sliver
of the brain displayed. By installing the Nvidia driver manually, we
made it work.
We have one Centos 5 machine where it is working (machine0
The problem with the NVIDIA driver installation is that it overwrites
the GL shared lib links and removes the default CentOS GL libs. If
you then do an update via up2date, yum, or whatever you use to keep
CentOS up to date and one of the packages updated is the GL one, then
the NVIDIA ones get o
Yes, that makes sense. But what libraries can I use to run tksurfer
-without- installing the Nvidia libraries?
Paul Raines wrote:
The problem with the NVIDIA driver installation is that it overwrites
the GL shared lib links and removes the default CentOS GL libs. If
you then do an update via
Brian,
Does the 'qdec' application run for you on Centos5?
Our apps do not require any particular graphics card. Through
experience, it seems the Nvidia cards give the least trouble (compared
to ATI), but we have never been able to track down exactly why
(something in the bowels of each manufa
Thank everyone for very informative comments!
I am a newbie in freesurfer myself, I just got a dataset for the
analysis (data was preprocessed in freesurfer), and since I am moving
myself toward doing any analysis in python, and the tools I use now are
python libraries, I wanted to load the data i
Hello,
I'm trying to use freesurfer to map the visual cortex and get region
borders of V1, V2.. etc.
We used a conventional rotating/expanding wedge paradigm, and I followed
the steps described in FsFastIndividualRetinotopy Analysis
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinot
Wait, you are copying the NVIDIA GL replacement libraries to machines that do
not have NVIDIA cards and the proprietary nvidia driver installed? ANd it
works? I would think no GL app would run in that case.
Maybe the NVIDIA GL libs are smart enough to handle the case they find
no NVIDIA car
Yes, qdec apparently works ok without the Nvidia driver libraries.
We want to run tksurfer remotely, so the video card won't really be
used. But apparently we need special functionality that does not exist
in the standard GL libraries.
Purchasing a video card just to get access to the driver
Well, yes, as a test I copied in the Nvidia GL libraries. For remote
VNC, it works. Locally, though, glxgears and glxinfo now give segfaults.
On the wiki, I see a downloadable version of vncserver.glx.
http://surfer.nmr.mgh.harvard.edu/fswiki/RemoteAccess
This version sets up which refers to s
At the Martinos Center, I have extracted the GL libraries from the Mesa
rpms and put them in those directories. When some one is using VNC
(or even doing remote X), it is better to use those libraries than
the ones that come with NVIDIA. Otherwise they do get errors. Which
is pretty much the o
Hi Nick,
I am just giving a try to the new mris_compute_lgi matlab script kindly
provided by Marie, and so far so good. I would appreciate the new binary for:
Mac OS X 10.5.2, linux_x86, and linux_x86_64.
Thanks a lot.
Martin
On Thursday 24 April 2008 18:40:12 Nick Schmansky wrote:
> Martin a
Martin,
The binary mris_fill for these OSs can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable
Nick
On Thu, 2008-04-24 at 20:43 +0200, Martin Kavec wrote:
> Hi Nick,
>
> I am just giving a try to the new mris_compute_lgi matlab script kindly
> p
Hi Yaroslav and Pádraig,
Please follow the link pasted below to get an alpha version of pymgh.
It requires the latest Python and Numpy.
https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/10224/1/2a5da2a125134fbdfc9e6850be1fcc09
(expires in 30 days )
Make sure PYTHONPATH has the d
Hello,
We want to get the percent signal change for the activated regions and for
that we want to use the h.nii and h-offset.nii files.
We plan to divide the h.nii by h-offset.nii .
First of all is this a correct approach?
Second, h.nii has 4 frames in it, which one do we really need?
Than
Yes, it is. The h.nii file has a somewhat tortured format. If you just
want the contrast as a percent, then look in the contast directory for
cespct.
Elif SIKOGLU wrote:
Hello,
We want to get the percent signal change for the activated regions and
for that we want to use the h.nii and h-of
Hi Yaroslav,
You can comment out those lines regarding GLoverride.
The real magic, as pointed out by Nick, is acutally the xf4vnc
that can be downloaded from http://sourceforge.net/projects/xf4vnc .
Tren
> On Mon, 2007-01-15 at 23:27 -0500, Yaroslav Halchenko wrote:
> Thank you very much for pr
Thank you Tren,
Actually Nick Schmansky at the time of original request pointed me out
(I believe in an offlist conversation) to xf4vnc, I have built it
then from CVS snapshot (there were/are no source tarballs), but it was
segfaulting. Debian maintainer of VNC packages unfortunately isn't
really
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