spm_global is not a good way of computing "globals" for VBM, as it was
intended to compute a kind of average brain intensity (by thresholding out
"non-brain" voxels, and computing the mean of what is left). It is better to
compute the volumes properly with the script below (although you may want to
take the absolute value, as it gives negative results if the data are stored
left-handed).
Best regards,
-John
On Thursday 04 August 2005 10:15, Jürgen Hänggi wrote:
> Hi Cyril
>
> Now it works! Thanks a lot?
> But there are two problems:
> 1. How to get the valid number of voxels!
> I have tried it with the following function from John:
>
> V = spm_vol(spm_get(1,'*c1*.img'));
> vol = 0;
> for i=1:V.dim(3),
> img = spm_slice_vol(V,spm_matrix([0 0 i]),V.dim(1:2),0);
> vol = vol + sum(img(:));
> end;
> fprintf('%g voxels, %g litres\n', vol, vol*det(V.mat(1:3,1:3))*1e-6);
>
> 2. The results seem to be invalid.
> e.g. 0.4954 * 327888 voxels (1mm*1mm*1mm) = 162435 and this is equal to
> 0.162 l
>
> I investigate the brains of AD patients and these brains are degenerated
> but only
> 0.162 l GM seems to be a too small volume in order to be a valid measure of
> GM volume.
>
> If I divide the number of voxels bei the value for the modulation then the
> volume seems
> to be more plausible:
> 327888 voxels (1mm*1mm*1mm) / 0.4954 = 0.662 l
>
> The corresponding result from the script of John is:
> 0.563 litre
>
> What do you think?
> Thanks a lot in advance
> Best regards
> Juergen
>
> > -----Ursprüngliche Nachricht-----
> > Von: Cyril Pernet [mailto:[log in to unmask]]
> > Gesendet: Donnerstag, 4. August 2005 07:55
> > An: Jürgen Hänggi
> > Betreff: Re: AW:Re: [SPM] GM/WM/CSF volume computation in SPM5b]
> >
> > Hi Jürgen
> >
> > well it's not an error ...
> >
> > > Hi Cyril
> > >
> > > Thanks a lot for your advice.
> > > But the function:
> > >
> > > spm_global(spm_vol('*.img'))
> > >
> > > does not work and I have no experience in M-file programing.
> >
> > to use that go into the directory where your image(s) is
> > (are) strored and type the function with the name like
> > spm_global(spm_vol('mwc1_jurgen*.img')) ;-) everything should be ok
> >
> > best
> > - cyril
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