Then its more complicated. When you say vertices and faces do you mean a tesselation? e.g. a Delaunay tesselation? Of the head volume or just the outer surface?
For volume (e.g. tetrahedrons) tesselations you could use:
t = tsearchn(X,TES,XI);
which returns NaN for points outside of the tesselation (actually outside of the convex hull in case of a Delaunay tesselation). I've tried this for some non-Delaunay derived tesselations but I'm not sure if that is allowed/100% correct so you should check. (you could also look at using [k,d]= dsearchn(X,TES,XI) which allows you to check for distance to your vertices for each point and then formulate a treshold).
If you only have vertices and faces for the boundary of the head (e.g. surface triangulation) then you could add a known inner point to which all triangles can form a valid tetrahedron and then create your own tesselation. But this may not work for all boundary triangles (I imagine it gets complicated at the ears).
Alternatively if you work with image/voxel coordinates only and you have the indices for the voxels in the head. Lets say these are IND and M is your 3D image matrix then you could create your image matrix containing nan's as follows:
M_nan=nan(size(M)); %Matrix filled with nan's the size of M M_nan(IND)=M(IND); %Replace entries at IND with M(IND)
Or if L is a logic array describing the head entries then simply M(~L)=nan;