#!/usr/bin/zsh
#Specify paths on your own

# The brain165a10f17 dataset was cropped to a 70 x 80 x 70 dataset 
# The following is the command line parameters to the "CropImageFilter" code.
# The cropped file is Brain165Cropped
#
# brain165a10f17 may be obtained if needed, from 
# ftp://public.kitware.com/pub/itk/Data/BrainWeb/BrainPart2.tgz

echo ./CropImageFilter.exe brainweb165a10f17.mha 55 70 55 56 67 55 Brain165Cropped.mhd;
 ./CropImageFilter.exe brainweb165a10f17.mha 55 70 55 56 67 55 Brain165Cropped.mhd;

# The cropped dataset is deformed by Thin plate splines to produce a 3D deformed
# dataset Brain165DeformedByTPS. To do the deformation, Thin Plate Splines were 
# used with 5 arbitratily chosen landmarks. The landmarks are in the file
# LandmarksTPS.txt.
#
# The file TPSWarp code also generates the deformation field produced by the TPS
# and the difference image.
 echo ./TPSWarp.exe LandmarksTPS.txt Brain165Cropped.mhd Brain165DeformedByTPS.mhd BrainDefFieldAfterTPS.mhd DiffOriginalVsTPSWarped.mhd;
 ./TPSWarp.exe LandmarksTPS.txt Brain165Cropped.mhd Brain165DeformedByTPS.mhd BrainDefFieldAfterTPS.mhd DiffOriginalVsTPSWarped.mhd;


 # Now we will try to register the deformed dataset (Brain165DeformedByTPS) to the
 # original dataset (Brain165Cropped). 
 #
 # The FEM registration parameters try to use Multiresolution registration, without
 # landmarks for now. You may include landmarks. They are listed in the file
 # FiniteElementRegistrationLandmarks3.txt
 #
 # The FEMReg1 code is nearly the same as the DeformableRegistration1.cxx code
 # with slight modifications so it runs on 3D. 
  ./FEMReg1.exe FiniteElementRegistrationParameters3.txt