CT2MNI152Affine.py

#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 29 16:02:52 2017

@author: pkao
"""

import os
import CTtools
from subprocess import call
import sys


#ct_scan_path = '/home/pkao/CT2MNI152/example/example1.nii.gz'

#ct_scan_path = '/media/pkao/Dataset/UC-Irvine/Angela/N17-13/20170823_131500UCISTRYKERMEDTRONICs007a003A.nii.gz'

ct_scan_path = str(sys.argv[1])

MNI_152_bone = os.path.join(os.getcwd(),'MNI152_T1_1mm_bone.nii.gz')

MNI_152 = os.path.join(os.getcwd(),'MNI152_T1_1mm.nii.gz')

bspline_path = os.path.join(os.getcwd(), 'Par0000bspline.txt')

nameOfAffineMatrix = ct_scan_path[:ct_scan_path.find('.nii.gz')]+'_affine.mat'

print('The location of MNI152 bone:' , MNI_152_bone)

# if you want to do ct scan removal 
#ct_scan_wodevice = CTtools.removeCTscandevice(ct_scan_path)

ct_scan_wodevice = ct_scan_path

ct_scan_wodevice_bone = CTtools.bone_extracted(ct_scan_wodevice)

call(['flirt', '-in', ct_scan_wodevice_bone, '-ref', MNI_152_bone, '-omat', nameOfAffineMatrix, '-bins', '256', '-searchrx', '-180', '180', '-searchry', '-180', '180', '-searchrz', '-180', '180', '-dof', '12', '-interp', 'trilinear'])

call(['flirt', '-in', ct_scan_wodevice, '-ref', MNI_152, '-applyxfm', '-init', nameOfAffineMatrix, '-out', ct_scan_wodevice[:ct_scan_wodevice.find('.nii.gz')]+'_MNI152.nii.gz'])

# the code below implement the deformable transformation

ct_scan_wodevice_contraststretching = CTtools.contrastStretch(ct_scan_wodevice)

call(['flirt', '-in', ct_scan_wodevice_contraststretching, '-ref', MNI_152, '-applyxfm', '-init', nameOfAffineMatrix, '-out', ct_scan_wodevice_contraststretching[:ct_scan_wodevice_contraststretching.find('.nii.gz')]+'_MNI152.nii.gz'])

call(['elastix', '-m', ct_scan_wodevice_contraststretching[:ct_scan_wodevice_contraststretching.find('.nii.gz')]+'_MNI152.nii.gz', '-f', MNI_152, '-out', os.path.dirname(ct_scan_path), '-p', bspline_path])