Extract the centerline of the structure using “Extract Centerline” extension’s “Centerline curve” output
Use Curved Planar Reformat to generate a new volume of slices perpendicular to the centerline curve.
Gather and average HU values in the reformatted volume
This last step could be done using a cylindrical tube down the center of the reformatted volume and the Segment Geometry module, or could be done by transforming your initial segmentation into the reformatted space (using the transform generated by the Curved Planar Reformat module) and using that segment in Segment Geometry (you might need to harden the transform and change the segmentation geometry to match the reformatted volume to get this to work correctly).