Hi Jake,
one way to do this is to use an area weighted sum. For example, if you want to calculate \int\Omega (v - v{obs})2 d\Omega, you can do (for a 2d mesh):
`%compute areas;
areas=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y);
%compute delta v on elements
deltav= (vx-vx_obs).2+(vy-vy_obs).2;
deltav_elem=deltav(md.mesh.elements)*[1;1;1]/3;
%Integrate over entire domain
J=sum(deltav_elem.*areas);`
I hope this helps!
Mathieu