Calculate the mean of region with nonzero pixels

2 min readMar 7, 2022

I have a mask with regions labeled with 1, 2 and 3. I have a 3D volume that I would like to calculate the mean of the pixels correspond to those regions.

I want to calculate the mean of the regions with number 1, number 2 and number 3 separately.

Is the following correct?

m = mean(volume(mask==1));

m = mean(volume(mask==2));

m = mean(volume(mask==3));

NOTE:-

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This requires a different approach altogether. You need to use one of the aggregating functions splitapply, accumarray or groupsummary. Assuming your mask is not a mask but a label image with integer values from 0 to N:

objectsmean = accumarray(double(mask(:))+1, yourimage(:), [], @mean);
%or
objectsmean = splitapply(@mean, yourimage(:), double(mask(:))+1);
%or
objectsmean = groupsummary(yourimage(:), mask, 'mean');

accumarray is probably the fastest. The double(..) is here in case your mask is stored as an integer type and the number of objects is equal to intmax(class(mask)) which would cause an overflow when 1 is added.

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