Hello All,
we are considering combining some data from the left and right hemispheres. Is
there a way to implement a transform of the spherical atlas Right --> Left
hemisphere? Topologically, this probably corresponds to turning the sphere
inside-out (plus registration of residual hemispheric d
Hi Guang,
it's because the partial-volume correction will be a bit different. Use the
one from the aseg.stats, as there's no reason to use the different wm
labels as different partial volume classes.
cheers
Bruce
On Thu, 17 Sep 2009, Guang Zeng wrote:
Hi, there,
I ran a subject through F
This is due to partial volume correction. Use the hippo volumes from
aseg.stats.
doug
Guang Zeng wrote:
> Hi, there,
>
> I ran a subject through FreeSurfer pipeline. I found that the size of
> left and right hippocampus in aseg.stats are
> larger than that of left and right hippocampus in wmpar
Hi, there,
I ran a subject through FreeSurfer pipeline. I found that the size of left and
right hippocampus in aseg.stats are
larger than that of left and right hippocampus in wmparc.stats after step. 3.
If I want to compare the FreeSurfer segmented hippocampus with a manually
traced hippoc
not sure what you mean. You can load the data into matlab and use the
matlab hist function to look at histograms. For example, from the subject's
mri directory:
[vaseg, M,mr] = load_mgh('aseg.mgz');
[vnorm, M,mr] = load_mgh('norm.mgz');
ind_wm = find(vaseg == 2);
ind_gm = find(vaseg == 3);
his
Hi,
Is there any tool or function to create a histogram to check if I am
distinguishing in the right way the white matter from the grey matter??
_
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Kelly Silva wrote:
> Hello,
> I would like to know:
> 1) How can I use the mri_binarize for the hippocampus? How are the
> input and output image that I have to put?
Did you look at the --help? It's pretty extensive.
> 2) How can I visualize (generate) an hippocampus mask to see with
Hi Kelly,
you should be able to use mri_extract_label aseg.mgz 17 53 hippo.mgz then
mri_tessellate to generate the lh (17) and rh (53) hippo surfaces.
cheers,
Bruce
On Thu,
17 Sep 2009, Kelly Silva wrote:
Hello,
I would like to know:
1) How can I use the mri_binarize for the hippoc
Hello,
I would like to know:
1) How can I use the mri_binarize for the hippocampus? How are the input
and output image that I have to put?
2) How can I visualize (generate) an hippocampus mask to see with
the tksurfer command?
Thanks a lot,
You can just use tksurfer, something like
tksurfer subject lh hippocampus
assuming you called it lh.hippocampus
There will be a lot of warnings/errors printed to the terminal. These
just have to do with the fact that the number of vertices will be
different than the cortical surfaces.
You can
Hi xiantong,
it depends on how well you match the acquisitions. We have found that if
you match them well then for the same field strength you can eliminate most
differences, but field strength still results in a small but measurable
bias (e.g. 3T vs. 1.5T). Check out Xiao Han's paper on our wi
Hi experts,
I want to know whether Freesurfer is able to eliminate effects from the data
obtained from different center with different NMR equipment.
As we know, the data obtained from different MRI equipments may be quite
different. Even the data from the same equipment but in different ac
yes, tkmedit will show it when you click on it (or when you mouse over)
On
Thu, 17 Sep 2009, africa millan wrote:
Sorry, I elaborate:
I would like to know the intensity of the voxel where I'm putting the control
point to check if the voxel belongs to the white matter or the grey one. Is
Sorry, I elaborate:
I would like to know the intensity of the voxel where I'm putting the control
point to check if the voxel belongs to the white matter or the grey one. Is
there any freesurfer tool to know it?
Af.
_
Con V
I'm not sure what you mean. tkmedit will tell you the intensity of every
voxel you either mouse over or click on
On Thu, 17 Sep 2009, africa millan
wrote:
Hello everybody
I would like to know if there is any way to check the grey intensity of each
voxel using tkmedit tools.This option cou
you can use mri_tessellate to create a mesh, then tksurfer will visualize
it
On Thu, 17 Sep 2009, Gonzalo Rojas Costa wrote:
> Dear Douglas:
>
> And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz
> with the mri_binarize command ?...
>
> Sincerely,
>
>
> Gonzalo Rojas Cos
Hello everybody
I would like to know if there is any way to check the grey intensity of each
voxel using tkmedit tools.This option could help me to distinguish in a better
way the white matter from the grey one.Thank you.
_
Des
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