Hello,

I'm trying to get the correlation between 2 maps.

I used the command:

measure correlation #2 in_map #1

I also saved the resampled map. Then, I wrote a very simple python code that calculates the correlation coefficient as following:

def compute_correlation(map1, map2):

threshold = np.percentile(map1.flatten(), 99) # top 1% value

mask = (map1 >= threshold) #& (map2 != 0)

values1 = map1[mask]

values2 = map2[mask]

corr = np.corrcoef(values1, values2)[0, 1]

return corr

Although it is considered masking as it is done in ChimeraX, I was never able to get the correlation value I got from ChimeraX. I got 0.1 from the python code and 0.68 in ChimeraX. Any suggestions?

Thank you

Muhamed Amin, Ph.D

Assistant Professor of Physics

University of Groningen,

Groningen, Netherlands