Hey Ariana,
A simple workflow would be -
- Crop the two images appropriately to exclude the dark areas (with intensity values 0) using the function imcrop
- From the description of your question, it's a bit unclear what exactly it is that you want out of correlation. Typically, the function corr2 returns the 2-D correlation coefficient as a scalar, the function corrcoeff returns a matrix of correlation coefficients, or you could also use xcorr2 which would return the spatial correlation of image1 with respect to image2.
The function that you finally end up using depends on the kind of output that you want out of correlation.
Hope this helps!
