“Equalize “Image Dimensions”, “Image Spacing” and “Image Origin” between CT and MRI images” => This should not be necessary
“Segment the phantom pipes in two CT and MR imaging” => You don’t need to segment anything. Instead, you can add landmarks at the intersection of planes and tubes. You cannot easily use tube points between planes, because you don’t know how much they are shifted along the tube’s centerline (physical planes do not appear as planar structures in the MRI). If planes are not visible on the MRI at all then you can change your phantom to contain a grid of tubes (don’t make all the tubes parallel). You may use all the tube curve points for validation
Scattered transform module is probably a good choice. The other option would be to compute thin-plate-spline transform using SlicerIGT extension’s Fiducial Registration Wizard module, but in case of hundreds of input points, this transform may be slow to compute.
You can apply transforms to any nodes using Transforms module.