How to run an algorithm on part of the image?

I want to detect structure of interest of an image by superpixel algorithm. First, I apply SLIC algorithm, which returns labeled matrix,to segment image into superpixels and then I want to apply same algorithm on some superpixels that I obtained. But since the shape of superpixels are amorphous I could not extract specific superpixels to apply the algorithm. Is there any Matlab function to do this?