Supposing you have a 3D grid Pixel_x, Pixel_y, Pixel_z, and you have Center_x, Center_y, Center_z, and Radii
Center_x_row = reshape(Center_x, 1, []);
Center_y_row = reshape(Center_y, 1, []);
Center_z_row = reshape(Center_z, 1, []);
Radiisq_row = reshape(Radii, 1, []).^2;
Pixel_x_col = reshape(Pixel_x, [], 1);
Pixel_y_col = reshape(Pixel_y, [], 1);
Pixel_z_col = reshape(Pixel_z, [], 1);
distssq = (Pixel_x_col - Center_x_row).^2 + (Pixel_y_col - Center_y_row).^2 + (Pixel_z_col - Center_z_row).^2;
pixel_within_sphere = distssq <= Radiisq_row;
num_pixel_within_sphere = sum(pixel_within_sphere);
and now you can take mean(num_pixel_within_sphere) and so on.
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