ENH: changed CLI parameter and added parameter files (issue SlicerPro…

…state#334)

* only using Parameters_BSpline.txt for now

SliceTracker/Resources/ElastixRegistrationParameters/Parameters_Affine.txt

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+// Example parameter file for affine 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.
+(MovingImageDimension 3)
+
+// 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")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+
+// These may be changed to Fixed/MovingSmoothingImagePyramid.
+// See the manual.
+(FixedImagePyramid "FixedRecursiveImagePyramid")
+(MovingImagePyramid "MovingRecursiveImagePyramid")
+
+// 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 "AffineTransform")
+(Metric "AdvancedMattesMutualInformation")
+
+// ***************** Transformation **************************
+
+// Scales the affine matrix elements compared to the translations, to make
+// sure they are in the same range. In general, it's best to  
+// use automatic scales estimation:
+(AutomaticScalesEstimation "true")
+
+// Automatically guess an initial translation by aligning the
+// geometric centers of the fixed and moving.
+(AutomaticTransformInitialization "true")
+
+// 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 )
+// 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:
+// 200-500 works usually fine for affine registration.
+// For more robustness, you may increase this to 1000-2000.
+(MaximumNumberOfIterations 250)
+
+// 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 1.0)
+
+// **************** 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 2048)
+
+// Refresh these spatial samples in every iteration, and select
+// them randomly. See the manual for information on other sampling
+// strategies.
+(NewSamplesEveryIteration "true")
+(ImageSampler "Random")
+
+// ************* 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
+// only interested in the final (nonrigidly) deformed moving image
+// for example.
+(WriteResultImage "true")
+
+// The pixel type and format of the resulting deformed moving image
+(ResultImagePixelType "short")
+(ResultImageFormat "mhd")
+
+

SliceTracker/Resources/ElastixRegistrationParameters/Parameters_BSpline.txt

@@ -0,0 +1,169 @@
+// 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.
+(MovingImageDimension 3)
+
+// 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")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Resampler "DefaultResampler")
+
+// These may be changed to Fixed/MovingSmoothingImagePyramid.
+// See the manual.
+(FixedImagePyramid "FixedRecursiveImagePyramid")
+(MovingImagePyramid "MovingRecursiveImagePyramid")
+
+// 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 "AdvancedMattesMutualInformation")
+
+// ***************** 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.
+(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.
+
+// 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 )
+// 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 500)
+
+// 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 1.0)
+
+// **************** 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 2048)
+
+// Refresh these spatial samples in every iteration, and select
+// them randomly. See the manual for information on other sampling
+// strategies.
+(NewSamplesEveryIteration "true")
+(ImageSampler "Random")
+
+// ************* 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 "short")
+(ResultImageFormat "mhd")
+
+