Also, I ran it on a Red Hat system and I'm still getting the error so I
don't think it is a machine specific problem. Any suggestions.
Thanks.
Anil.
On 2/14/07, Anil Roy <[EMAIL PROTECTED]> wrote:
Here are the details of the acquisitions:
Images acquired on a 3T Signa scanner with a standard
Here are the details of the acquisitions:
Images acquired on a 3T Signa scanner with a standard GE head coil. 3D
T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec,
TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix)
The machine has 4 gigs of RAM. Also, AFNI is able to t
Anil,
I was able to successfully run -autorecon1 (after performing my own tal
alignment). This included the skullstrip.
How much memory does your machine have? It needs to have at least 2GB.
Nick
On Wed, 2007-02-14 at 15:49 -0600, Anil Roy wrote:
> Nick,
>
> The files were acquired axially(
Anil,
On this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
there is a TIFF image of some example scans having decent contrast.
Nick
On Wed, 2007-02-14 at 17:03 -0500, Bruce Fischl wrote:
> can you tell us the details of the acquisition? The contrast is
> intrinsic
Hello all,
This is an error I got while running the longitudinal
analysis on one of our subjects.It didnt create the
filled.mgz volume and so the surfaces weren't created.
[EMAIL PROTECTED] Fill Tue Feb 13 20:59:04 MST 2007
/ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri
mri_fill -a ../script
can you tell us the details of the acquisition? The contrast is
intrinsic, and it has to be sufficient for g/w segmentation.
On Wed, 14 Feb
2007, Anil Roy wrote:
Nick,
The files were acquired axially(120 slices) on a GE scanner. These scans are
a couple of years old. I should also inform yo
Nick,
The files were acquired axially(120 slices) on a GE scanner. These scans are
a couple of years old. I should also inform you that I converted the orginal
120 slices into afni brik format (afni was able to read them) and then used
mri_convert to convert the BRIK to cor. Freesurfer then used
Anil,
Can you send me the orig.mgz file? You can upload it to my email
address via:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Wed, 2007-02-14 at 14:54 -0600, Anil Roy wrote:
> Hi All,
>
> I followed the steps in the tutorial on tkregister2 to align the two
> vo
Jenifer,
The 32bit version of the tools will also work on 64bit systems. But
I've just uploaded the 64bit centos versions for you if you want those.
Goto:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
and get:
mris_volume_x86_64.tar.gz
and copy to your $FREESURFER_HOME/bin and type:
tar zx
I have a question regarding editing the pial surface. Many times it
includes bright spots, such as fat or vessels. Should I be editing this
out? I'm pretty clear on getting rid of included dura, but if I spent the
time to edit out every little bright spot, it would be pretty time
intensive. Wou
Hi, when I use mri_anatomical stats - I get a total WM value 503450 for
left and right hemispheres
that's the same number in the stats file in the stats folder.
but when I use mris_wm_volume - I get 174896 and 178464
which one is the accurate one?
also, is the GM volume I get from mris_anatomica
Marie Schaer wrote:
Dear Doug Greve,
Many thanks for your reply, however when I overlay group1.mgh and
group2.mgh on my average subject, they look pretty similar.
So I read it in matlab, using load_mgh(group*.mgh), which gave me
files having exactly the same structure as beta.mgh (size
Recently (7 Feb 2007) mris_wm_volume for 32bit centos was posted in
/pub/dist.
Is there any possibility of posting 64bit centos versions of
mris_wm_volume & mris_volume?
I'm running Freesurfer 3.0.4
Many Thanks,
Jenifer
___
Freesurfer mailin
something like:
mri_surf2surf --s subject --hemi lh --sval input --tval output --fwhm 5
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I'm attempting to do thickness analysis based on the guide at:
http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf
For the smoothing part usin
Hi, I'm attempting to do thickness analysis based on the guide at:
http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf
For the smoothing part using mri_surf2surf (page 14), I was wondering
what a typical command line should look like.
Thanks,
-Aaron-
did you look at the surface? You'll probably need to either fix the
watershed, or manually disconnect the cerebellum
On Wed, 14 Feb 2007, Alex
Fornito wrote:
Is there anything that can be done? (e.g., tweaking certain parameters)
Alex Fornito
JN Peters Research Fellow
Melbourne Neuropsychiatr
Dear Doug Greve,
Many thanks for your reply, however when I overlay group1.mgh and
group2.mgh on my average subject, they look pretty similar.
So I read it in matlab, using load_mgh(group*.mgh), which gave me
files having exactly the same structure as beta.mgh (size of 23406 x
1 x 7 x 6)
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