Par0011 - elastix

Registration Description

intrapatient (sometimes intra-sheep); B-spline transformation; normalized correlation

Image data

• 3D chest CT
• Lung
• 20 scans
• Voxel size mostly 0.7x0.7x~0.7 mm, four scans with thicker slices 1.25, 1.5, 2, 2.5 mm.
• Dimension: on average about 400 x 300 x 350

Screen shots:

Application

Registration of intra-patient pulmonary CT scans for the EMPIRE10 challenge at MICCAI. Sometimes sheep lungs.

For more information visit the EMPIRE10 website.

The results of the challenge can be found here.

Registration Settings

For parameter files see the Elastix Model Zoo repository on GitHub.

elastix version: 4.301

Command line calls:

elastix -f scans/x_Fixed.mhd  -m scans/x_Moving.mhd  -p parameters.Par0011.affine.txt   -out outDir1_x

elastix -f scans/x_Fixed2.mhd -m scans/x_Moving2.mhd -p parameters.Par0011.bspline1.txt -out outDir2_x
    -t0 outDir1_x/TransformParameters.0.txt

elastix -f scans/x_Fixed2.mhd -m scans/x_Moving2.mhd -p parameters.Par0011.bspline2.txt -out outDir3_x
    -t0 outDir2_x/TransformParameters.0.txt -fMask lungMasks/x_Fixed.mhd

where x refers to the patient number (01 - 20), and Fixed2 and Moving2 to slightly pre-processed versions of the fixed and moving image.

Published in

These registration are described in the publication:

Marius Staring, Stefan Klein, Johan H.C. Reiber, Wiro J. Niessen and Berend C. Stoel, Pulmonary Image Registration With elastix Using a Standard Intensity-Based Algorithm, EMPIRE10 workshop at MICCAI.

References

© 2020 Viktor van der Valk