Coordinate transformations?

Hello, I am attempting to fully automate the vmtkcenterline function by specifying seed points like this: vmtkcenterlines -seedselector pointlist -sourcepoints 0 0 0 -targetpoints 1 1 1 2 2 2. To find the source and target points I have a function that utilizes gradient data and the mask as nifti files, it then finds the end points. I have checked its functionality by looking at the output points on the mask file using itk snap. Unfortunately, I have found that after segmentation and level sets, and smoothing my .vtp file has a different coordinate system. For reference the endpoints from the .nii file are: (131.15801614763552, 80.82237600922723, 17)
(47.65384615384615, 137.34615384615384, 644)
(97.26470588235294, 75.5672268907563, 678)
and the .vtp file are (roughly):
(159, 55, -113)
(129, 75, 105)
(147, 54, 117)
How are the coordinates transformed using the vmtk pipeline? Any info on how to convert my scripts .nii endpoints to the .vtp endpoints would be greatly appreciated


You can have a look how it got fully automated in 3D Slicer’s Extract Centerline module. See source code here.