Dear Shashwath, 

What are the original volumes in WFU pickatlas then?

BW, Alexander

-----------------------------

Alexander Hammers, MD PhD

Chair in Functional Neuroimaging
Neurodis Foundation
http://www.fondation-neurodis.org/
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Visiting Reader; Honorary Consultant Neurologist
Division of Neuroscience and Mental Health, Faculty of Medicine
Imperial College London, UK
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Honorary Reader in Neurology; Honorary Consultant Neurologist
Department of Clinical and Experimental Epilepsy
National Hospital for Neurology and Neurosurgery/ Institute of Neurology, University College London, UK

On 28 nov. 2011, at 22:04, Shashwath Meda wrote:

I created my binary masks using the WFU pickatlas and then resliced them to the dimensions of my input images. Yes, they contain both hemispheres.

On Mon, Nov 28, 2011 at 3:03 PM, Christian Lambert <[log in to unmask]> wrote:

Two questions - How have you defined your ROIs? Does your binary image contain both amygdalae?

- Chris

On 28 Nov 2011, at 20:17, Shashwath Meda <[log in to unmask]> wrote:

> Hi All - I am in the process of extracting bilateral amygdala volumes from modulated GM images across my subjects processed using the VBM8 toolbox. I am using the below script to do the same, in doing so i see that on average the amydala volumes across my subjects are grossly overestimated (6000 mm3) using this as opposed to a more reasonable estimate of 2000mm3-3000mm3 that I derived using Freesurfer. I would appreciate any input pn this?
>
>  Vmask=spm_vol(spm_select(1,'image','Select the binary mask'));
> Vdata=spm_vol(spm_select(Inf,'image','Select modulated warped GM'));
> volume= zeros(numel(Vdata),1);
>
> for j=1:numel(Vdata),
>    tot = 0;
>    for i=1:Vdata(j).dim(3),
>        M    = spm_matrix([0 0 i]);
>        img  = spm_slice_vol(Vdata(j),M,Vdata(j).dim(1:2),0);
>        Mmsk = Vmask.mat\Vdata(j).mat*M;
>        mask = spm_slice_vol(Vmask,Mmsk,Vdata(j).dim(1:2),0);
>        img  = img.*mask;
>        img(~isfinite(img)) = 0;
>        tot = tot + sum(img(:));
>    end
>    voxvol    = abs(det(Vdata(j).mat))/100^3;
>    volume(j) = tot*voxvol;
> end
>
> disp(volume)
>
> --
> with regards,
>
> Shashwath Meda
>
> ***********************************************
> Imaging Genetics Analyst III
> 515-F Light Hall
> Vanderbilt University Medical Center
> Cell: (313) 505-6847
> Off: (615) 875-3086
>
> ***********************************************
>

--
with regards,

Shashwath Meda

***********************************************
Imaging Genetics Analyst III

515-F Light Hall

Vanderbilt University Medical Center
Cell: (313) 505-6847
Off: (615) 875-3086

***********************************************