Dear Abhinay,
You could also try with IBASPM toolbox (Individual Brain Atlases using
Statistical Parametric Mapping (SPM) Software).
This is a toolbox developed in SPM5 and SPM2, and you can get it in SPM
extensions web page (http://www.fil.ion.ucl.ac.uk/spm/ext/) or you can
type directly in the google search engine IBASPM and you can get it
directly.
The version of this toolbox works very well but if you are very
interested in using it just let us know and we can send you the last
update, which has not been uploaded yet.
ISBASPM gives the structure volume of the structures predefined in a
specific Atlas. The most used is the AAL giving to you a volume of the
116 structures that includes hippocampus.
Like all automatic methods this is not accurately enough, and like Ged
Rigway said a semiautomatic or manual segmentation will be closer to the
truth.
I hope this helps,
Regards,
Lester.
Lester Melie Garcia
Head of Neuroinformatics Department
Cuban Neuroscience Center
Calle 25 esq. 158, Cubanacan. Playa
Havana. Cuba
Phones: (53-7)-208 4460
(53-7)-271 7442
Fax : (53-7)- 2086707
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Ged Ridgway
Sent: lunes, 15 de enero de 2007 7:49
To: [log in to unmask]
Subject: Re: [SPM] FLAIR
Hi Abhinay,
> 1) How to get good FLAIR templates in SPM
I think the easiest way around this would be to use SPM5's unified
segmentation, which just uses tissue probability maps, and doesn't
assume any particular intensity relationship between these and the
images.
You may still have problems if e.g. the gray/white contrast is
inadequate (I don't have much experience with FLAIR, but some of the
images I've seen have rather unclear GM/WM boundaries), but then I
don't think there's much you could do about that within SPM.
> 2) how to measure hippocampus volume by using SPM?
Well, SPM is designed *not* to do this kind of volumetry. The idea
with SPM is that you analyse e.g. the whole GM across subjects, and if
they have significant volume differences in the hippocampus then
hopefully this gets picked up in the resulting statistical maps.
You could define a rough hippocampal ROI in MNI space and use SPM
(with small volume correction for FWE p-values), but this will still
amount to looking for significant voxel-wise hippocampal differences,
rather than measuring volume.
To measure volume, you really need to segment the hc on each scan. You
could try using an automatic segmentation propagation method for this
(e.g. the SPM extension AAL -- http://www.cyceron.fr/freeware/ or
perhaps something like FreeSurfer http://surfer.nmr.mgh.harvard.edu/
which I've heard has good seg prop parcellation as well as cortical
analysis).
However, you might find that these aren't accurate enough, in which
case I think your only option is to manually (or "semi-automatically")
segment the hc. You could try e.g. itk-SNAP for this
http://www.itksnap.org/
Best,
Ged.
