Hi Tamir,
I understand that you want to calculate the average correlation coefficients in each of the masked regions as specified by the mask file.
Since your mask is a binary file you can use the find function in the mask file to access the indices on the data file. Based on the indices you can assign each range of indices to a specific Matrix and perform the correlation by using the corrcoef function. Refer to this answer and this answer for more information of correlations on multi-dimensional matrices.
One example on using the find function is as shown below, assuming a 2-D mask and a 2-D image,
a = [0 0 0 0;0 0 1 1;0 0 1 1;0 0 0 0]; % Mask'
b = rand(4,4); % data
idx = find(a); % find mask locations
c = b(idx); % data points at the mask
Kiran Felix Robert
