Hi Mojdeh
Have you checked out Koen van Leemput's hippocampal fled segmentation that you
can run through recon-all? It might do what you want automatically.
Cheers
Bruce
On Dec 19, 2012, at 4:07 PM, Mojdeh Zamyadi wrote:
> Hi there,
>
> Sorry, if my question is confusing. This is what I want
Hi there,
Sorry, if my question is confusing. This is what I want to do, I have
two groups of controls and patients and I've already run recon-all on
them. I now want to know the head/body/tail volumes. What I did was:
1. used "mri_binarize" to get the right and left hippocampal masks from
the cor
No, they are not in any atlas space. The space is "native" in that 1mm
in the image represents 1mm in the subject's brain. Therefore, you can
directly compare the hippo volume across subjects.
doug
On 12/18/2012 12:59 PM, Mojdeh Zamyadi wrote:
> Hi Doug,
>
> Thanks for the quick reply. I actual
Hi Mojdeh
they are not in atlas space and the volumes are for that subject, so you
shouldn't have to do anything if I understand you correctly
cheers
Bruce
On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote:
> Hi Doug,
>
> Thanks for the quick reply. I actually saw this link before first
> posting my q
Hi Doug,
Thanks for the quick reply. I actually saw this link before first
posting my question but it doesn't quite answer my question. What I want
to know is whether the T1.mgz & aseg.mgz files are in an atlas space? if
that's the case, it means the segmentation for all my subjects are in
the
Hi Mojdeh, try looking at this doc
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug
On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
> Hi all,
>
> I want to segment the hippocampus into head/body/tail in itk SNAP using
> the hippocampus mask that I create from the result of recon-al
Hi all,
I want to segment the hippocampus into head/body/tail in itk SNAP using
the hippocampus mask that I create from the result of recon-all
segmentation. My question is, are the T1.mgz and aseg.mgz files in the
native space of the image or in the atlas space? I know the voxel size
is diffe
