Bit of a long shot this because my doxygen is a bit rusty, but have you tried
\cond \endcond
around the header section. (Conditional inclusion, but blank = false)
For example, the standard C or C++ headers usually clutter the dependency graph pretty much, so you might want to remove them from that graph (as their usage can be considered as part of the language). You can do that on a file basis like this (tested with 1.8.7):
/// \cond
#include <iostream>
#include <string> // whatever...
/// \endcond
In other instances this excludes the code between the markers from being visible to doxygen, but I'm unsure it will work for this instance.