Manual registration using elastix
ibtissam Essadik
Hello,
I'm trying to use elastix Tool for the registration (Affine transformation ) of the two 3D images.
After used elastix command line, I obtain a parameter file and a Registered image generated by elastix.
My aim is to use this matrix transformation & center of rotation existed in the parameter file to register the moving image and get a Registered image similar to the one obtained by elastix. However, my manually registration results were always a little bit different from elastix generated.
I am wondering if I missed something in the transformation matrix or i didn't apply it correctly.
Any suggestions are greatly appreciated.
My Python script:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import SimpleITK as sitk
import cv2
import nibabel as nib
from scipy.spatial import distance
from statistics import mean
from pandas import DataFrame
path_vol1 = "C:/Users/Essadik/Desktop/DATA_IRMs/TOF_BET/Vol1_bet.nii"
vol = sitk.GetArrayFromImage(sitk.ReadImage(path_vol1))
img_transformed = np.zeros((vol.shape[0],vol.shape[1],vol.shape[2]))
img_transformed.shape
matrice=np.array([[1.026340 ,-0.075878 ,0.019792,6.766561],
[0.019973 ,1.058883 ,0.128099,-4.116563 ],
[-0.067282 ,-0.205729 ,1.053152 ,6.330935],
[0, 0, 0,1]])
center = np.array([[1, 0,0, -0.3606814668], [0, 1,0, 12.8406273633] ,[0, 0,1, 0.2839643048], [0, 0, 0,1]] )
center_inverse = np.array([[1, 0,0, 0.3606814668], [0, 1,0, -12.8406273633], [0, 0,1, -0.2839643048], [0, 0, 0,1]] )
total_matrix = center @ matrice @ center_inverse
for i in range(vol.shape[0]):
for j in range(vol.shape[1]):
for k in range(vol.shape[2]):
k_xfm,j_xfm,i_xfm, _ = total_matrix @ np.array([k,j, i,1])
pixel_data = 0
if( k_xfm >= 0 and k_xfm < vol.shape[2] and j_xfm >=0 and j_xfm < vol.shape[1] and i_xfm >=0 and i_xfm < vol.shape[0] ):
pixel_data = vol[int(i_xfm), int(j_xfm),int(k_xfm)]
img_transformed[i, j,k] = pixel_data
new_img=img_transformed.astype(np.uint16)
img_recal = sitk.GetImageFromArray(new_img)
sitk.WriteImage(img_recal, "vol1_manual_reg1.mha")
The transform file:
(Transform "AffineTransform")
(NumberOfParameters 12)
(TransformParameters 1.026340 -0.075878 0.019792 0.019973 1.058883 0.128099 -0.067282 -0.205729 1.053152 6.766561 -4.116563 6.330935)
(InitialTransformParametersFileName "NoInitialTransform")
(HowToCombineTransforms "Compose")
// Image specific
(FixedImageDimension 3)
(MovingImageDimension 3)
(FixedInternalImagePixelType "float")
(MovingInternalImagePixelType "float")
(Size 512 512 192)
(Index 0 0 0)
(Spacing 0.3515625000 0.3515625000 0.5000032187)
(Origin -96.0032653809 -73.2788696289 -42.7602081299)
(Direction 0.9979060389 -0.0646703700 -0.0011317127 0.0645305101 0.9966330591 -0.0505802205 0.0043989440 0.0504012784 0.9987193602)
(UseDirectionCosines "true")
// AdvancedAffineTransform specific
(CenterOfRotationPoint -0.3606814668 12.8406273633 0.2839643048)
// ResampleInterpolator specific
(ResampleInterpolator "FinalBSplineInterpolator")
(FinalBSplineInterpolationOrder 3)
// Resampler specific
(Resampler "DefaultResampler")
(DefaultPixelValue 0.000000)
(ResultImageFormat "mhd")
(ResultImagePixelType "short")
(CompressResultImage "false")
Best regards,
M.St...@lumc.nl
Dear Ibtissam,
You could inspect the source code of this transformation to know what happens precisely:
With kind regards,
Marius Staring
Sent: 19 November 2020 4:26 PM
To: elastix-imageregistration
Subject: [elastix-imageregistration] Manual registration using elastix
Hello,
I'm trying to use elastix Tool for the registration (Affine transformation ) of the two 3D images.
After used elastix command line, I obtain a parameter file and a Registered image generated by elastix.
My aim is to use this matrix transformation & center of rotation existed in the parameter file to register the moving image and get a Registered image similar to the one obtained by elastix. However, my manually registration results were always a little bit different from elastix generated.
I am wondering if I missed something in the transformation matrix or i didn't apply it correctly.
My Python script:
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