July 2010 Image Registration Techniques, Benchmarking, Strategy Surgical Planning Laboratory Center for Neurological Imaging July 2010 Lidwien Veugen Supervision by Dominik S. Meier, PhD

July 2010 Contents - Introduction Image Registration, 3D Slicer - Theory Transformations, Similarity Metrics - Benchmarking Time/Memory vs Iterations/Samples - Registration Strategies - Registration Cases Brains, PET-CT, EMPIRE10

July 2010 Introduction Image Registration: - Process of matching multiple image by optimal transformation 3D Slicer: - Free Open Source Software program - Huge amount of Registration Modules/Methods

July D Slicer

July 2010 Theory Transformations Mapping points from original spatial coordinates to new spatial coordinates: (u,v,w) = T{(x,y,z)} Rigid Transform Rotation + Translation (u,v,w) = R*(x,y,z) + t 6 DOF Affine Transform Rotation + Translation + Scaling + Shear (u,v,w) = A*(x,y,z) + t 12 DOF

July 2010 Theory Transformations BSpline Spline: function defined piecewice by polynomials Cubic grid of moving control points describes deformation 3 DOF per control point BrainsDemonWarp Thirion + Maxwell: Image registration based on optical flow Boundaries are semi-permeable membranes with effectors/demons High DOF

July 2010 Theory Transformation BRAINSFit - Rigid, Affine, BSpline - Mutual Information - 6/12/higher DOF Expert Automated Registration - Pipelines: Rigid, Affine, BSpline - MutualInfo + MeanSqE + NormCorr - 6/12/higher DOF Plastimatch - Pipeline: Rigid/Affine, BSpline(s) - MutualInfo + MeanSqE - 6/12/higher DOF

July 2010 Theory Similarity Metrics Tells to what degree two images are aligned Based on: intensity, landmarks Mutual Information - Measure of the statistical dependence between two random variables: Information about image A that is shared by B and vice versa - Maximized if the two images are spatially aligned - Based on Shannon entropy H: measure of intensity prediction - Fast measure

July 2010 Theory Similarity Metrics Normalized Cross Correlation - Based on cross correlation - Maximized if the two images are spatially aligned - Intra-patient + Intra-modality - Time consuming Mean Squared Difference - Summation of the squared differences between two images - Minimized if the two images are spatially aligned - Intra-patient + Intra-modality - Time consuming

July 2010 Theory Optimization Optimization algorithm: Tries to find a global solution to an energy function - Gradient descent - Statistical optimization - Line search algorithm - One-plus-one evolutionary - Multiresolution

July 2010 Registration Accuracy Subtraction Fixed - Moving Registered Checkerboard Alternating squares from fixed and moving image

July 2010 Benchmarking Effect of the amount of iterations and samples on CPU time and memory for different modules/methods Rigid: 4 methods Affine: 7 methods BSpline: 2 methods Default: Samples = 10000, Iterations = 200 Iterations: 11 values, ranging from 25 to Samples: 20 values, ranging from 25 to

July 2010 Benchmarking Fast results with: SPL Dell Linux Cluster of 50 computers  Creates log-file of every job  Matlab

July 2010 Benchmarking Results

July 2010 Benchmarking Results Time vs Iterations - Not much effect - Increase: Brainsfit, Exp.Autom. - Decrease: Multiresolution - Constant: BSpline modules Time vs Samples - Increase: All modules, except: - Decrease: Exp.Autom. NormCr - 10  800 seconds (0.003%  13%) - Rigid < Affine < BSpline Memory vs Iterations Not much effect - Increase: All modules, except: - Constant: Brainsfit, Multires - Lowest: 2MB; Highest: 155MB Memory vs Samples - Increase: All modules, except: - Decrease: Exp.Autom. NormCr - Lowest: Rigid (10-100MB) - Highest: BSpline ( MB)

July 2010 Registration Cases Slicer Registration Case Library

July 2010 Registration Strategies Choice of Transformation Modality, Subject, Inter/Intra, Part of body Choice of Similarity Metric Inter/Intra, Time/Accuracy Focus Time/Accuracy/Memory  Sim.metric/iterations/samples Fixed Image Resolution/Contrast

July 2010 Registration Cases EMPIRE10 Evaluation of Methods for Pulmonary Image Registration 2010 = Challenge of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 20 Pairs of chest CT scans: variety scanners, voxel size, breathing phase Evaluation: Lung boundaries, Fissures, Landmarks, Singularities

July 2010 Registration Cases

July 2010 Registration Cases EMPIRE10 - Registration Pipeline: 1.Fast Affine Registration 2.Fast nonrigid Bspline Registration (grid = 7) 3.Fast nonrigid Bspline Registration (grid = 12) 4.Fast nonrigid Bspline Registration (grid = 17) 5.BrainsDemonWarp

July 2010 Registration Cases EMPIRE10 - Quality Registration Subtraction + MATLAB help in evaluation registration: Median pixelvalue of absolute subtracted image: the lower the better

July 2010 Registration Cases fMRI alignment to structural scan (T1) - Fixed: T1 scan (anatomical reference) - Moving: fMRI scan - Problem: Low tissue contrast, acquisition related distortions Registration based on ventricles only

July 2010 Registration Cases Aging Mobility Study 2 year follow-up - 2 Exams at different times: nonrigid (BSpline) - Incorrect axis-info - Fixed: MPRAGE - Moving: T2, FLAIR

July 2010 Registration Cases Inter-subject Normal brain MIDASexample - Fixed: T1 - Moving: T2, MRA - Interpatient: non-rigid (BSpline)

July 2010 Registration Cases PET-CT Fusion 2 - Intersubject: nonrigid BSpline, BrainsDemonWarp - Fixed: CT-scan patient 1 - Moving: CT-scan patient 2 - Problem: Different posture

July 2010 Registration Cases Brain Intersubject PNL-XNAT - Intersubject: nonrigid (BSpline) - Problems with (too much) BSpline

July 2010 Registration Cases Brain Intersubject OrientationFlx - Intersubject: nonrigid (BSpline) - Fixed: T1 - Moving: T2 - Problems with nested transformations

July Fixed: Colin27 - Moving: Patient - Orientation! Registration Cases Brain Intersubject Dartmouth Montreal Neurological Institue: Colin27 for group analysis in MRI studies

July 2010 Acknowledgements Finally, I would like to thank everybody from CNI for the possibility to do an internship here! Thanks to my supervisor Dominik S. Meier, PhD

July 2010 Questions? ?