How do I tell matlab to identify vertices within ROI?

I want matlab to identify all vertices of the hexagons that will be within an ROI. That ROI can be of any shape (it can be an irregular shape).

Here is my code:

l=12;
    k=14;
    C=rand(l,k);
    xhex=[0 1 2 2 1 0]; 
    yhex=[2 3 2 1 0 1]; 

    for i=1:k
        j=i-1;
        for q=1:l
            m=q-1;
            patch((xhex+mod(q,2))+2*j,yhex+2*m,C(q,i)) 
            hold on
        end
    end
    axis equal


h = drawfreehand;

I have attached a picture of a sample ROI.

I will appreciate any advise on this matter. Many thanks.

[Image Analyst]

This would be so easy with a digital image. Just use h.createMask and bwmorph and find(). But using an analytical image created with patch or fill or whatever, it's trickier (at least for me).