I can see how to extract mean scalar value for a segment from the segment statistics, but what I would like to do is extract this for each MRI slice- in a similar way to how the segment cross-sectional area outputs area for each slice. Is it possible?
Can you write a bit about your use case? What is the clinical application?
You can implement this either in a short Python script or enhance the Segment cross-sectional area module to take an additional input volume and get the mean value for each slice (it is a single line of Python code to get average intensity of a masked volume at a specific slice, you just need to propagate the selected volume to the
run method and save the result in an additional table in the column).
Thank you for your reply. I am wanting to use the mean intensity from fat/water MRI to calculate muscle fat infiltration. I can see this is possible from the segment statistics output, however I want to examine this slice-by-slice in addition to whole segment (muscle) that the segment statistics allows.