Hi Donald and everybody,
I created AAL .mgh and .label-s in FS Colin27 space, if anybody is
interested please drop me a line.
best regards!
Gari
On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald
mclaren.don...@gmail.comwrote:
Has anyone created an AAL label file for Freesurfer? I've done some
Hi Daniel
it looks like you have too much wrap in your image, with a significant
amount of brain wrapping to the top. Nothing will work on this
sorry
Bruce
On Tue, 23 Oct 2012, Daniel Ferreira
wrote:
Hi Nick,
Here comes attached the tkmedit orig.mgz
thanks
Daniel
2012/10/22 Nick
Dear Freesurfer people,
We posted this question before, but maybe you missed it. We have a question
regarding the relationship between cortical volume, cortical area and cortical
thickness measurements derived from the parcellation stat-file. We were under
the impression that the volume is
Hi Masise and Laura, yes, it is area*thickness, but area*thick is
computed on a vertex-by-vertex basis, then summed over vertices. This is
not the same as summing the area and multiplying it by the mean of the
thickness.
doug
On 10/23/2012 06:52 AM, L. Koenders wrote:
Dear Freesurfer people,
Hi Verena - Which version of freesurfer are you using? In the public
release of 5.1 the CVS registration option in trac-all is disabled.
a.y
On Tue, 23 Oct 2012, Verena Gramse wrote:
From: Verena Gramse
Sent:
Hi Anastasia,
Ahh.. I used the regular 5.1 and pointed to our dev folder where the cvs_avg35
(and cvs_avg_inMNI152) live.
So, do you recommend skipping cvs registration for now?
Thanks in advance!
Verena
From: Anastasia Yendiki
Dear FreeSurfers,
I am processing MEMPRAGE images:
1) I use the RMS (of the echoes) output from the scanner
2) the echoes were converted to mgz format [memprage_echo1(to4).mgz],
conformed to 256³ , 1mm isotropic, and no further processing.
3) I ran the mris_make_surfaces -dura
Hi Bruce.
I know I can set the value 110 to the voxels corresponding to white matter
lesions, using the FreeSurfer environment.
The issue is that I have binary masks for each subject. These masks are
binary files that match each subject in native space. Thus, for each
subject, this mask contains
probably the best thing to do is to fill the lesion with the average of
the values on the border. That will create a minimal amount of new
gradients in the image
cheers
Bruce
On Tue, 23 Oct 2012, Julio Alberto González Torre
wrote:
Hi Bruce.
I know I can set the value 110 to the voxels
I'm attempting to remove some dura which is affecting my surfaces, but upon
completion of running gcut I can see no differences in my images, nor can I
use tkmedit to view my T1 with brainmask.gcuts.mgz, because it says it
couldn't import the segmentation volume. I looked for brainmask.gcuts.mgz
Check your log. If gcut detects that the gcutted brain is much smaller than the
original brain, it will assume that something bad has happened and it won't
write brainmask.gcuts.mgz. This may be what is happening in your case. To fix
this, you can adjust the watershed threshold or add something
How do I extract a color table from an annotation?
Thanks,
Anisha
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Anisha,
You can use mris_anatomical_stats with the -c option to extract the
color table from an annotation.
Best,
Maritza
On Tue, 23 Oct 2012, Anisha Keshavan wrote:
How do I extract a color table from an annotation?
Thanks,
Anisha
___
Mark,
I've posted the recon-all that will be used in the upcoming v5.2, which
contains the fix whereby control points are no longer used in the aseg,
here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
you can copy it to your v5.1 distro, but note i've named it
Hi,
Does anyone have any advice for compiling freesurfer on Linux powerPC
architectures?
I've managed to compile a 64-bit version of freesurfer on Linux PowerPC, and
I'd be happy to post the documentation for the compile process I used - if I
could be sure it would build usable binaries :-(
Tony,
the powerpc is a big-endian processor, so make sure the BYTEORDER gets
defined as 4321 by configure (see a Makefile). see dcm.c for code that
depends on endianness and make sure the big-endian code gets compiled.
i dont think the configure.in script is smart enough to setup the endian
Hello everyone,
I'm conducting an analysis involving a training group and a control
group, where each group has a pre and a post scan. I setup the matrix file,
the contrast file, and ran mri_glmfit along with mri_glmfit-sim for the
cluster correction. The analysis finished revealing a
Hi,
I was wondering if we can compare functional connectivity between
blocks within a run as we do for BOLD signal using freesurfer. Current
documentation of freesurfer is for resting state and does not consider
conditions that experiment is Blocked Design.
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