Dear SPMers:
I am new to VBM and I am doing VBM to compare 2 groups of subjects, following the analyzing steps in John Ashburner's VBM tutorial (use DARTEL in spm8). John leaves the "trivial" step of inputting total intracranial volume (TIV) in the 2nd level model, and I can't figure it out. In addition, by checking the list, I got more confused.
Simplify, for 2 subjects in each of the two groups, TIVs are:
group1 group2
sbj1 2.01 2.06
sbj2 2.11 1.99
I want to do a two-sample t-test.
Question1
John's tutorial says to input TIVs in "Global values"->"User"->"Global values". But spm says "Global values" should be a X-by-1 array. And there's no option to input two TIVs for the two groups respectively. How should I input TIVs?
Question2
Some posts said traditionally, TIVs are input as covariates. Is it correct I do as below?
Covariate
Vector: 2.01 2.11
Name: group1
Interactions: None
Centering: (default) Overall mean. I have no idea what this is, should I change it to "Factor 1 mean", or "No centering"?
Covariate
Vector: 2.06 1.99
Name: group2
Interactions: None
Centering: (default) Overall mean.
Question3:
I am using John's script (below) to calculate TIV. I figure "Vols" is the returned volume. For one subject, I got GM/WM/CSF as 0.92/0.71/0.38, and TIV was the sum, 2.02. Are these values normal? (I am just wondering the sum may be near 1).
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
Looking forward to your replies.
Thanks
Xiang
|