Add parameter file for liver strain analysis paper

models/Par0065/Parameters0065_Affine.txt

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+(AutomaticParameterEstimation "true")
+(AutomaticScalesEstimation "true")
+(CheckNumberOfSamples "true")
+(DefaultPixelValue 0)
+(FinalBSplineInterpolationOrder 3)
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(ImageSampler "RandomCoordinate")
+(Interpolator "LinearInterpolator")
+(MaximumNumberOfIterations 256)
+(MaximumNumberOfSamplingAttempts 8)
+(Metric "AdvancedMattesMutualInformation")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(NewSamplesEveryIteration "true")
+(NumberOfResolutions 4)
+(NumberOfSamplesForExactGradient 4096)
+(NumberOfSpatialSamples 2048)
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Registration "MultiResolutionRegistration")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+(ResultImageFormat "nii")
+(Transform "AffineTransform")
+(WriteIterationInfo "false")
+(WriteResultImage "true")

models/Par0065/Parameters0065_Bspline.txt

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+// Example parameter file for B-spline registration
+// C-style comments: //
+
+// The internal pixel type, used for internal computations
+// Leave to float in general. 
+// NB: this is not the type of the input images! The pixel 
+// type of the input images is automatically read from the 
+// images themselves.
+// This setting can be changed to "short" to save some memory
+// in case of very large 3D images.
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+
+// The dimensions of the fixed and moving image
+// NB: This has to be specified by the user. The dimension of
+// the images is currently NOT read from the images.
+// Also note that some other settings may have to specified
+// for each dimension separately.
+//no longer needed(FixedImageDimension 2)
+//(MovingImageDimension 2)
+
+// Specify whether you want to take into account the so-called
+// direction cosines of the images. Recommended: true.
+// In some cases, the direction cosines of the image are corrupt,
+// due to image format conversions for example. In that case, you 
+// may want to set this option to "false".
+(UseDirectionCosines "true")
+
+// **************** Main Components **************************
+
+// The following components should usually be left as they are:
+//(Registration "MultiResolutionRegistration")
+(Registration "MultiMetricMultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+
+// These may be changed to Fixed/MovingSmoothingImagePyramid.
+// See the manual.
+//(FixedImagePyramid "FixedRecursiveImagePyramid")
+//(MovingImagePyramid "MovingRecursiveImagePyramid")
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+
+// The following components are most important:
+// The optimizer AdaptiveStochasticGradientDescent (ASGD) works
+// quite ok in general. The Transform and Metric are important
+// and need to be chosen careful for each application. See manual.
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "BSplineTransform")
+
+//(Metric "AdvancedMeanSquares")
+(Metric "AdvancedNormalizedCorrelation")
+//(Metric "AdvancedMattesMutualInformation")
+
+
+//(Metric "AdvancedMattesMutualInformation" "BendingEnergyPenalty")
+//(Metric "TransformBendingEnergyPenalty" "AdvancedMattesMutualInformation")
+
+//(Metric0Weight 1.0)
+//(Metric1Weight 0.1)
+//Metric1RelativeWeight
+
+// ***************** Transformation **************************
+
+// The control point spacing of the bspline transformation in 
+// the finest resolution level. Can be specified for each 
+// dimension differently. Unit: mm.
+// The lower this value, the more flexible the deformation.
+// Low values may improve the accuracy, but may also cause
+// unrealistic deformations. This is a very important setting!
+// We recommend tuning it for every specific application. It is
+// difficult to come up with a good 'default' value.
+(FinalGridSpacingInVoxels 4)
+//(FinalGridSpacingInPhysicalUnits 8)
+//(FinalGridSpacingInPhysicalUnits 16)
+
+
+// Alternatively, the grid spacing can be specified in voxel units.
+// To do that, uncomment the following line and comment/remove
+// the FinalGridSpacingInPhysicalUnits definition.
+//(FinalGridSpacingInVoxels 16)
+
+// By default the grid spacing is halved after every resolution,
+// such that the final grid spacing is obtained in the last 
+// resolution level. You can also specify your own schedule,
+// if you uncomment the following line:
+//(GridSpacingSchedule 4.0 4.0 2.0 1.0)
+// This setting can also be supplied per dimension.
+
+(GridSpacingSchedule 8 8 8 4.0 4.0 4.0 2.0 2.0 2.0 1.0 1.0 1.0)
+
+// Whether transforms are combined by composition or by addition.
+// In generally, Compose is the best option in most cases.
+// It does not influence the results very much.
+(HowToCombineTransforms "Compose")
+
+// ******************* Similarity measure *********************
+
+// Number of grey level bins in each resolution level,
+// for the mutual information. 16 or 32 usually works fine.
+// You could also employ a hierarchical strategy:
+//(NumberOfHistogramBins 16 32 64)
+(NumberOfHistogramBins 32)
+
+// If you use a mask, this option is important. 
+// If the mask serves as region of interest, set it to false.
+// If the mask indicates which pixels are valid, then set it to true.
+// If you do not use a mask, the option doesn't matter.
+(ErodeMask "false")
+
+// ******************** Multiresolution **********************
+
+// The number of resolutions. 1 Is only enough if the expected
+// deformations are small. 3 or 4 mostly works fine. For large
+// images and large deformations, 5 or 6 may even be useful.
+(NumberOfResolutions 4)
+
+// The downsampling/blurring factors for the image pyramids.
+// By default, the images are downsampled by a factor of 2
+// compared to the next resolution.
+// So, in 2D, with 4 resolutions, the following schedule is used:
+//(ImagePyramidSchedule 8 8  4 4  2 2  1 1 )
+// And in 3D:
+//(ImagePyramidSchedule 8 8 8  4 4 4  2 2 2  1 1 1 )
+
+(ImagePyramidSchedule 8 8 8 4 4 4 2 2 2 1 1 1)
+
+// You can specify any schedule, for example:
+//(ImagePyramidSchedule 4 4  4 3  2 1  1 1 )
+// Make sure that the number of elements equals the number
+// of resolutions times the image dimension.
+
+// ******************* Optimizer ****************************
+
+// Maximum number of iterations in each resolution level:
+// 200-2000 works usually fine for nonrigid registration.
+// The more, the better, but the longer computation time.
+// This is an important parameter!
+//(MaximumNumberOfIterations 5000)
+//(MaximumNumberOfIterations 1000)
+(MaximumNumberOfIterations 2000)
+//(MaximumNumberOfIterations 2000)
+//(MaximumNumberOfIterations 2500)
+//(MaximumNumberOfIterations 3000)
+
+// The step size of the optimizer, in mm. By default the voxel size is used.
+// which usually works well. In case of unusual high-resolution images
+// (eg histology) it is necessary to increase this value a bit, to the size
+// of the "smallest visible structure" in the image:
+(MaximumStepLength 0.3)
+
+// **************** Image sampling **********************
+
+// Number of spatial samples used to compute the mutual
+// information (and its derivative) in each iteration.
+// With an AdaptiveStochasticGradientDescent optimizer,
+// in combination with the two options below, around 2000
+// samples may already suffice.
+//(NumberOfSpatialSamples 500)
+//(NumberOfSpatialSamples 1000)
+//(NumberOfSpatialSamples 2000)
+//(NumberOfSpatialSamples 3000)
+(NumberOfSpatialSamples 4000)
+//(NumberOfSpatialSamples 5000)
+
+// Refresh these spatial samples in every iteration, and select
+// them randomly. See the manual for information on other sampling
+// strategies.
+(NewSamplesEveryIteration "true")
+(ImageSampler "RandomCoordinate")
+
+// ************* Interpolation and Resampling ****************
+
+// Order of B-Spline interpolation used during registration/optimisation.
+// It may improve accuracy if you set this to 3. Never use 0.
+// An order of 1 gives linear interpolation. This is in most 
+// applications a good choice.
+(BSplineInterpolationOrder 1)
+
+// Order of B-Spline interpolation used for applying the final
+// deformation.
+// 3 gives good accuracy; recommended in most cases.
+// 1 gives worse accuracy (linear interpolation)
+// 0 gives worst accuracy, but is appropriate for binary images
+// (masks, segmentations); equivalent to nearest neighbor interpolation.
+(FinalBSplineInterpolationOrder 3)
+
+//Default pixel value for pixels that come from outside the picture:
+(DefaultPixelValue 0)
+
+// Choose whether to generate the deformed moving image.
+// You can save some time by setting this to false, if you are
+// not interested in the final deformed moving image, but only
+// want to analyze the deformation field for example.
+(WriteResultImage "true")
+
+// The pixel type and format of the resulting deformed moving image
+(ResultImagePixelType "float")
+(ResultImageFormat "mha")
+
+

models/Par0065/Parameters0065_Rigid.txt

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+(AutomaticParameterEstimation "true")
+(AutomaticScalesEstimation "true")
+(CheckNumberOfSamples "true")
+(DefaultPixelValue 0)
+(FinalBSplineInterpolationOrder 3)
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(ImageSampler "RandomCoordinate")
+(Interpolator "LinearInterpolator")
+(MaximumNumberOfIterations 256)
+(MaximumNumberOfSamplingAttempts 8)
+(Metric "AdvancedMattesMutualInformation")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(NewSamplesEveryIteration "true")
+(NumberOfResolutions 4)
+(NumberOfSamplesForExactGradient 4096)
+(NumberOfSpatialSamples 2048)
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Registration "MultiResolutionRegistration")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+(ResultImageFormat "nii")
+(Transform "EulerTransform")
+(WriteIterationInfo "false")
+(WriteResultImage "true")

models/Par0065/README.md

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+# Registration parameters for strain liver analysis.
+
+###  Registration Description
+interpatient; rigid, affine and bspline transform; advanced cross correlation
+
+
+###  Image data
+
+ - 3D MRI T1 Data healthy volunteers
+ - Liver
+ - 3 different states: end-expiration, end-inspiration, drinking of 1.5l of water
+ - Resolution: 1.5x1.5x3mm^3
+
+###  Application
+
+These parameters are used to register the livers at end-inspiration and 1.5l water drinking to end-expiration. From the deformation field volumetric strain and octahedral shear strain [1] is determined.
+
+###  Registration settings
+
+Livers are aligned using rigid transform first. Next an affine and bspline transform is performed on the livers.
+
+- Elastix version: 5.0.0
+- ITKElastix version: 0.21.0
+
+Python call:
+
+Do rigid transform:
+`
+elastix_object = itk.ElastixRegistrationMethod.New(fixed_image, moving_image)
+elastix_object.SetParameterObject(parameter_object_rigid)
+elastix_object.UpdateLargestPossibleRegion()
+transformed_image = elastix_object.GetOutput()
+transformed_parameters = elastix_object.GetTransformParameterObject()
+`
+
+Do affine, bspline transfrom:
+`
+elastix_object = itk.ElastixRegistrationMethod.New(fixed_image, transformed_image)
+elastix_object.SetParameterObject(parameter_object_affine_bspline)
+elastix_object.UpdateLargestPossibleRegion()
+transformed_image = elastix_object.GetOutput()
+transformed_parameters = elastix_object.GetTransformParameterObject()
+`
+
+###  Published in
+
+Noah Jaitner, Yasmine Safraou, Matthias Anders, Jakob Schattenfroh, Tom Meyer, Biru Huang, Jakob Jordan, Oliver Boehm, Alfonso Caiazzo, Tobias Schaeffter, Jing Guo, Ingolf Sack (2024), Non-invasive assessment of portal pressure by combined measurement of volumetric strain and stiffness of in vivo human liver (submitted)
+
+###  References
+
+[1] McGarry, M.D.J., et al., An octahedral shear strain-based measure of SNR for 3D MR elastography. Physics in Medicine and Biology, 2011. 56(13): p. N153-N164.