Cortical organisation is based on the principles of functional specialisati
on and functional integration. Those two concepts exist at multiple spatial
scales. For example at a macroscopic level, functionally segregated areas
V1 and V5 are integrated within the dorsal visual stream. At a microscopic
level, it is possible to infer the functional integration of (segregated) o
cular dominance columns within area V1. At the macroscopic level functional
specialisation and integration can be tested with functional neuroimaging,
using fMRI/PET or EEG/MEG. A framework that allows making inferences on fu
nctional integration between brain regions using fMRI will be presented. Th
e common feature of all techniques within that framework is that they can i
ncorporate second order terms and therefore explicitly allow for contextual
modulations. Two examples demonstrate how attention and paired associates
learning can modulate effective connectivity within the visual system. Furt
hermore these models can incorporate non-linear modulatory (feedback) conne
ctions that can account for the changes in effective connectivity observed.