Dear Dana,
Is there any difference to calculate the ICV with modulated segments (e.g. mwc1, mwc2, mwc3) and original segments (e.g. c1, c2, c3)? Am I right to guess there is no big differences since the modulated segments reflect the preserved amounts, i.e., the absolute volumes?
I've been using a script found in SPM archives, with the search keywords "grey matter volume and sum and isfinite" (see below). I wonder where may I find the "get_integrals" script as you mentioned in your email?
Sorry to add more questions on this post, but thanks for your answers!
Best wishes,
Meikei
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V = spm_vol(spm_select(Inf,'Image'));
Vols = zeros(numel(V),1);
for j=1:numel(V),
tot = 0;
for i=1:V(1).dim(3),
img = spm_slice_vol(V(j),spm_matrix(...
[0 0 i]),V(j).dim(1:2),0);
img = img(isfinite(img)); % <-- exclude non-finite values
tot = tot + sum(img(:));
end;
voxvol = abs(det(V(j).mat))/100^3; % volume of a voxel, in litres
Vols(j) = tot*voxvol;
end
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________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] On Behalf Of Perantie, Dana [[log in to unmask]]
Sent: Thursday, June 10, 2010 11:51 PM
To: [log in to unmask]
Subject: Re: [SPM] Do I need an ICV covariate for DARTEL + VBM?
Hi John,
If you would have used the ICV as a covariate in the old VBM, then you can do the same if you're using DARTEL. DARTEL is just a different method of registration. It just depends what you are interested in or what you want to report - absolute volumes or volumes relative to ICV. You can get total GM, WM, and CSF by summing all the values of the modulated segments (get_integrals). The result should be nearly identical to what you got before, but I would re-do it with the DARTEL images to make sure you are covarying the more relevant, exact amount.
-Dana
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of John McLean
Sent: Thursday, June 10, 2010 7:06 AM
To: [log in to unmask]
Subject: [SPM] Do I need an ICV covariate for DARTEL + VBM?
Hi,
Do I need to include ICV as a covariate for DARTEL + VBM? If so, how should I get the GM/WM/CSF estimate from DARTEL? More detial below...
I previously did some VBM analysis using the 'Old' unified segmenation approach during which I used the volumes for GM/WM and CSF to obtain a ICV covariate in the subsequent VBM analysis.
I am now reprocesing the data using DARTEL. I don't observe that there is a GM/WM/CSF volume textual output during this procedure. How do I obtain such an output, can I use the 'old' ICV output, or don't I need to include ICV as a covariate for VBM where the data has been pre-processed with DARTEL?
Any advice about the best approach would be welcome!
Many thanks
John
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