Centerline extraction with the “Tree” method should work even if the shape is not very elongated:
If you share an example segmentation (upload the .seg.nrrd file somewhere and post the link here) then I can confirm.
Have you tried to use the SegmentGeometry extension? It can give you the coordinates of the centroid points along a reslice axis, which is exactly what you are looking for. The only possible inconvenience is that these centroid positions are reported in voxel coordinate system of the resampled volume, so if you need the centroid positions in RAS coordinate system then you’ll need to multiply voxel coordinates by IJKtoRAS matrix of the resampled volume.
