I tried to draw this diagram
rpapa's showed me how to start by posting code to draw the 3 big boxes with circles at the top and the labels on the left and the arrows between them. That was a great help.
I've managed to modify that code to colour some of the elements. I've also created a new command which starts drawing the big box at the bottom and makes some of the connections between the circles in this box and the ones in the boxes above. However, I can't figure out how to draw the connection from the Thalamus box to the circle in the Amygdala because that arrow needs to go from the border of the big box and not from one of the circles inside it.
How can I draw a connection from the edge of the big box rather than from one of the circles?
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{positioning,calc,fit}
\begin{figure*}[!ht]
\centering
\newcommand{\bloc}[2]{
\begin{scope}[shift={#1}]
\begin{scope}[every node/.style={circle, draw, minimum size=2em}]
\node[circle, draw] [blue](#2-c1){};
\node[below left=1em of #2-c1][blue](#2-c2){};%to draw a circle inside a box
\node[below left=1em of #2-c2][blue](#2-c3){};
\node[below left=1em of #2-c3][blue](#2-c4){};
\end{scope}
\node[above left=1em and 0em of #2-c1][blue](#2-tt){#2};%to label the box by names Thalamus,Sensory Cortex
\node[draw,fit=(#2-c1) (#2-c2) (#2-c3) (#2-c4) (#2-tt)][red](#2){};%to draw a boxes
\end{scope}
}
\newcommand{\blocwithSum}[2]{
\begin{scope}[shift={#1}]
\begin{scope}[every node/.style={circle, draw, minimum size=2em}]
\node[circle, draw] [red](#2-c1){};
\node[below left=1em of #2-c1][red](#2-c2){};
\node[below left=1em of #2-c2][red](#2-c3){};
\node[below left=1em of #2-c3][red](#2-c4){};
\node[below right=2em and 1em of #2-c1][blue](#2-sum){\large $\Sigma$};
\end{scope}
\node[above left=1em and 0em of #2-c1][red](#2-tt){#2};%to label a box by name Orbitofrontal
\node[draw,fit=(#2-c1) (#2-c2) (#2-c3) (#2-c4) (#2-tt) (#2-sum)][blue](#2){};%to draw a box
\draw[->,red,thick] (#2-c1)-|(#2-sum);%to draw connection lines to sum
\draw[->,red,thick] (#2-c2)--++(2em,0) --(#2-sum);
\draw[->,red,thick] (#2-c3)--++(2em,0) --(#2-sum);
\draw[->,red,thick] (#2-c4)-|(#2-sum);
\end{scope}
}
\newcommand{\blocwithz}[2]{
\begin{scope}[shift={#1}]
\begin{scope}[every node/.style={circle, draw, minimum size=2em}]
\node[circle, draw][cyan] (#2-c1){};
\node[below left=1em of #2-c1][cyan](#2-c2){};%to draw circles
\node[below left=1em of #2-c2][cyan](#2-c3){};
\node[below left=1em of #2-c3][cyan](#2-c4){};
\node[below left=1 em of #2-c4](#2-c5){};
\node[below right=2em and 1em of #2-c1][red](#2-sum){\large $\Sigma$};%to draw Sum
% \node[below right=2em and 0 em of#2-sum](#2-sums){\large$\Sigma$};
\end{scope}
\node[above left=1em and 0em of #2-c1][cyan](#2-tt){#2}; %to label the box name Amagydala
\node[draw,fit=(#2-c1) (#2-c2) (#2-c3) (#2-c4) (#2-c5) (#2-tt) (#2-sum)][cyan](#2){}; %to draw the box
\draw[->,cyan,thick] (#2-c1)-|(#2-sum);%to draw connection lines to Sum
\draw[->,cyan,thick] (#2-c2)--++(2em,0) --(#2-sum);
\draw[->,cyan,thick] (#2-c3)--++(2em,0) --(#2-sum);
\draw[->,cyan,thick] (#2-c4)-|(#2-sum);
\end{scope}
}
\begin{tikzpicture}
\bloc{(0,0)}{Thalamus} %the position of box 1
\bloc{(4cm,0)}{Sensory Cortex} %the position of box 2
\blocwithSum{(9cm,0)}{Orbitofrontal Cortex} %the position of box 3
\blocwithz{(4cm,-7cm)}{Amygdala} % the position of box 4
\foreach \ii in{1,2,3,4} {
\node[draw][red](E\ii) at (Thalamus-c\ii-|-5,0){$S_{\ii}$};%to draw the inputs stimulus and their position
\draw[->,thick][blue] (E\ii)-- (Thalamus-c\ii);
\draw[->,thick] [red](Thalamus-c\ii) -- (Sensory Cortex-c\ii);
\draw[->,thick] [blue] (Sensory Cortex-c\ii) -- (Orbitofrontal Cortex-c\ii);
\draw[->,thick] [red] (Sensory Cortex-c\ii) -- (Amygdala-c\ii);
%\draw[->,thick] [red] (g) -- (Amygdala-c\ii);
}
\end{tikzpicture}
\caption{ Routes of limbic system}
\label{FB2}
\end{figure*}
\end{document}
Here's what I've got, building on rpapa's answer:
Thalamus box to the circle in the Amygdala– CroCo Nov 22 '15 at 3:16