See my image segmentation tutorial where I crop out objects using their bounding boxes. http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862
I believe it gives coordinates on the half pixel to eliminate any ambiguity about whether the bounding box is the inclusive box, or one pixel layer outside that. So you can use ceil() and floor() to make it do it either way depending on what you prefer.
