how to change grid value of data to make smooth spatial plot?

I have 40 brightness temperature(BT) data(mat files) of size 2805*2816 and latitude,longitude of same size.Each value of the BT is 4*4 Km^2 resolution.i want to make that of 200*200 km^2 resolution.i have chosen two steps :

1.For a particular 2D data point,40 data will be available for 40 files.have to take median value to make one file out of 40 files.

2.For the final file,I have to take the median value of each 50*50 square and have to put the median value on corresponding square instead of all varied values inside the square. PLEASE HELP.Thanks