Hi Isabel,
You pass in a three dimensional image volume the same way you pass in a two dimensional image. Here is an example:
load mri;
D = padarray(squeeze(D),[5 5 5]); %make bigger
D2 = imtranslate(D,[2.7 -5.1 1.5]); %Translate the image a little bit so imregister has to work
[optim metric]= imregconfig('monomodal'); %build the optimizer
mr = imregister(D2,D,'rigid',optim,metric); %register
imtranslate can be found here.
