.TH mia\-3dserial\-nonrigid 1 "v2.4.7" "USER COMMANDS" .SH NAME mia\-3dserial\-nonrigid \- Serial registration of 3D images. .SH SYNOPSIS .B mia\-3dserial\-nonrigid \-i [options] .SH DESCRIPTION .B mia\-3dserial\-nonrigid This program runs the image registration of a consecutively numbered image series. The registration is run in a serial manner, this is, only images in temporal succession (i.e. consecutive numbers) are registered, and the obtained transformations are applied accumulated to reach full registration. .SH OPTIONS .SS File-IO .RS .IP "\-i \-\-in-file=(required, input); string" input perfusion data set .IP "\-o \-\-out-file=(output); string" file name for registered fiels .RE .SS Registration .RS .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" Optimizer used for minimization For supported plugins see PLUGINS:minimizer/singlecost .IP "\-l \-\-mg-levels=3" multi\-resolution levels .IP "\-f \-\-transForm=spline" transformation type For supported plugins see PLUGINS:3dimage/transform .IP "\-r \-\-ref=\-1" reference frame (\-1 == use image in the middle) .RE .SS Help & Info .RS .IP "\-V \-\-verbose=warning" verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: .RS 10 .I trace \(hy Function call trace .RE .RS 10 .I debug \(hy Debug output .RE .RS 10 .I info \(hy Low level messages .RE .RS 10 .I message \(hy Normal messages .RE .RS 10 .I warning \(hy Warnings .RE .RS 10 .I fail \(hy Report test failures .RE .RS 10 .I error \(hy Report errors .RE .RS 10 .I fatal \(hy Report only fatal errors .RE .IP " \-\-copyright" print copyright information .IP "\-h \-\-help" print this help .IP "\-? \-\-usage" print a short help .IP " \-\-version" print the version number and exit .RE .SS Processing .RS .IP " \-\-threads=\-1" Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (\-1: automatic estimation). .RE .SH PLUGINS: 1d/spacialkernel .TP 10 .B cdiff Central difference filter kernel, mirror boundary conditions are used. .P .RS 14 (no parameters) .RE .TP 10 .B gauss spacial Gauss filter kernel, supported parameters are: .P .RS 14 .I w = 1; uint in [0, inf) .RS 2 half filter width. .RE .RE .TP 10 .B scharr This plugin provides the 1D folding kernel for the Scharr gradient filter .P .RS 14 (no parameters) .RE .SH PLUGINS: 1d/splinebc .TP 10 .B mirror Spline interpolation boundary conditions that mirror on the boundary .P .RS 14 (no parameters) .RE .TP 10 .B repeat Spline interpolation boundary conditions that repeats the value at the boundary .P .RS 14 (no parameters) .RE .TP 10 .B zero Spline interpolation boundary conditions that assumes zero for values outside .P .RS 14 (no parameters) .RE .SH PLUGINS: 1d/splinekernel .TP 10 .B bspline B-spline kernel creation , supported parameters are: .P .RS 14 .I d = 3; int in [0, 5] .RS 2 Spline degree. .RE .RE .TP 10 .B omoms OMoms-spline kernel creation, supported parameters are: .P .RS 14 .I d = 3; int in [3, 3] .RS 2 Spline degree. .RE .RE .SH PLUGINS: 3dimage/combiner .TP 10 .B absdiff Image combiner 'absdiff' .P .RS 14 (no parameters) .RE .TP 10 .B add Image combiner 'add' .P .RS 14 (no parameters) .RE .TP 10 .B div Image combiner 'div' .P .RS 14 (no parameters) .RE .TP 10 .B mul Image combiner 'mul' .P .RS 14 (no parameters) .RE .TP 10 .B sub Image combiner 'sub' .P .RS 14 (no parameters) .RE .SH PLUGINS: 3dimage/cost .TP 10 .B lncc local normalized cross correlation with masking support., supported parameters are: .P .RS 14 .I w = 5; uint in [1, 256] .RS 2 half width of the window used for evaluating the localized cross correlation. .RE .RE .TP 10 .B mi Spline parzen based mutual information., supported parameters are: .P .RS 14 .I cut = 0; float in [0, 40] .RS 2 Percentage of pixels to cut at high and low intensities to remove outliers. .RE .RE .RS 14 .I mbins = 64; uint in [1, 256] .RS 2 Number of histogram bins used for the moving image. .RE .RE .RS 14 .I mkernel = [bspline:d=3]; factory .RS 2 Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I rbins = 64; uint in [1, 256] .RS 2 Number of histogram bins used for the reference image. .RE .RE .RS 14 .I rkernel = [bspline:d=0]; factory .RS 2 Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .TP 10 .B ncc normalized cross correlation. .P .RS 14 (no parameters) .RE .TP 10 .B ngf This function evaluates the image similarity based on normalized gradient fields. Given normalized gradient fields $ _S$ of the src image and $ _R$ of the ref image various evaluators are implemented., supported parameters are: .P .RS 14 .I eval = ds; dict .RS 2 plugin subtype (sq, ds,dot,cross). Supported values are: .RS 4 .I ds \(hy square of scaled difference .RE .RS 4 .I dot \(hy scalar product kernel .RE .RS 4 .I cross \(hy cross product kernel .RE .RE .RE .TP 10 .B ssd 3D image cost: sum of squared differences, supported parameters are: .P .RS 14 .I autothresh = 0; float in [0, 1000] .RS 2 Use automatic masking of the moving image by only takeing intensity values into accound that are larger than the given threshold. .RE .RE .RS 14 .I norm = 0; bool .RS 2 Set whether the metric should be normalized by the number of image pixels. .RE .RE .TP 10 .B ssd-automask 3D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are: .P .RS 14 .I rthresh = 0; double .RS 2 Threshold intensity value for reference image. .RE .RE .RS 14 .I sthresh = 0; double .RS 2 Threshold intensity value for source image. .RE .RE .SH PLUGINS: 3dimage/filter .TP 10 .B bandpass intensity bandpass filter, supported parameters are: .P .RS 14 .I max = 3.40282e+38; float .RS 2 maximum of the band. .RE .RE .RS 14 .I min = 0; float .RS 2 minimum of the band. .RE .RE .TP 10 .B binarize image binarize filter, supported parameters are: .P .RS 14 .I max = 3.40282e+38; float .RS 2 maximum of accepted range. .RE .RE .RS 14 .I min = 0; float .RS 2 minimum of accepted range. .RE .RE .TP 10 .B close morphological close, supported parameters are: .P .RS 14 .I hint = black; string .RS 2 a hint at the main image content (black|white). .RE .RE .RS 14 .I shape = [sphere:r=2]; factory .RS 2 structuring element. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .TP 10 .B combiner Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: .P .RS 14 .I image =(required, input, io) .RS 2 second image that is needed in the combiner. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I op =(required, factory) .RS 2 Image combiner to be applied to the images. For supported plug-ins see PLUGINS:3dimage/combiner .RE .RE .RS 14 .I reverse = 0; bool .RS 2 reverse the order in which the images passed to the combiner. .RE .RE .TP 10 .B convert image pixel format conversion filter, supported parameters are: .P .RS 14 .I a = 1; float .RS 2 linear conversion parameter a. .RE .RE .RS 14 .I b = 0; float .RS 2 linear conversion parameter b. .RE .RE .RS 14 .I map = opt; dict .RS 2 conversion mapping. Supported values are: .RS 4 .I copy \(hy copy data when converting .RE .RS 4 .I linear \(hy apply linear transformation x -> a*x+b .RE .RS 4 .I range \(hy apply linear transformation that maps the input data type range to the output data type range .RE .RS 4 .I opt \(hy apply a linear transformation that maps the real input range to the full output range .RE .RS 4 .I optstat \(hy apply a linear transform that maps based on input mean and variation to the full output range .RE .RE .RE .RS 14 .I repn = ubyte; dict .RS 2 output pixel type. Supported values are: .RS 4 .I bit \(hy binary data .RE .RS 4 .I sbyte \(hy signed 8 bit .RE .RS 4 .I ubyte \(hy unsigned 8 bit .RE .RS 4 .I sshort \(hy signed 16 bit .RE .RS 4 .I ushort \(hy unsigned 16 bit .RE .RS 4 .I sint \(hy signed 32 bit .RE .RS 4 .I uint \(hy unsigned 32 bit .RE .RS 4 .I slong \(hy signed 64 bit .RE .RS 4 .I ulong \(hy unsigned 64 bit .RE .RS 4 .I float \(hy floating point 32 bit .RE .RS 4 .I double \(hy floating point 64 bit .RE .RS 4 .I none \(hy no pixel type defined .RE .RE .RE .TP 10 .B crop Crop a region of an image, the region is always clamped to the original image size in the sense that the given range is kept., supported parameters are: .P .RS 14 .I end = [[4294967295,4294967295,4294967295]]; streamable .RS 2 end of cropping range, maximum = (\-1,\-1,\-1). .RE .RE .RS 14 .I start = [[0,0,0]]; streamable .RS 2 begin of cropping range. .RE .RE .TP 10 .B dilate 3d image stack dilate filter, supported parameters are: .P .RS 14 .I hint = black; string .RS 2 a hint at the main image content (black|white). .RE .RE .RS 14 .I shape = [sphere:r=2]; factory .RS 2 structuring element. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .TP 10 .B distance Evaluate the 3D distance transform of an image. If the image is a binary mask, then result of the distance transform in each point corresponds to the Euclidian distance to the mask. If the input image is of a scalar pixel value, then the this scalar is interpreted as heighfield and the per pixel value adds to the distance. .P .RS 14 (no parameters) .RE .TP 10 .B downscale Downscale the input image by using a given block size to define the downscale factor. Prior to scaling the image is filtered by a smoothing filter to eliminate high frequency data and avoid aliasing artifacts., supported parameters are: .P .RS 14 .I b = [[1,1,1]]; 3dbounds .RS 2 blocksize. .RE .RE .RS 14 .I bx = 1; uint in [1, inf) .RS 2 blocksize in x direction. .RE .RE .RS 14 .I by = 1; uint in [1, inf) .RS 2 blocksize in y direction. .RE .RE .RS 14 .I bz = 1; uint in [1, inf) .RS 2 blocksize in z direction. .RE .RE .RS 14 .I kernel = gauss; factory .RS 2 smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize.. For supported plug-ins see PLUGINS:1d/spacialkernel .RE .RE .TP 10 .B erode 3d image stack erode filter, supported parameters are: .P .RS 14 .I hint = black; string .RS 2 a hint at the main image content (black|white). .RE .RE .RS 14 .I shape = [sphere:r=2]; factory .RS 2 structuring element. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .TP 10 .B gauss isotropic 3D gauss filter, supported parameters are: .P .RS 14 .I w = 1; int in [0, inf) .RS 2 filter width parameter. .RE .RE .TP 10 .B gradnorm 3D image to gradient norm filter .P .RS 14 (no parameters) .RE .TP 10 .B growmask Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if the have a lower intensity that is above the given threshold., supported parameters are: .P .RS 14 .I min = 1; float .RS 2 lower threshold for mask growing. .RE .RE .RS 14 .I ref =(required, input, io) .RS 2 reference image for mask region growing. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I shape = 6n; factory .RS 2 neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .TP 10 .B invert intensity invert filter .P .RS 14 (no parameters) .RE .TP 10 .B isovoxel This filter scales an image to make the voxel size isometric and its size to correspond to the given value, supported parameters are: .P .RS 14 .I interp = [bspline:d=3]; factory .RS 2 interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I size = 1; float in (0, inf) .RS 2 isometric target voxel size. .RE .RE .TP 10 .B kmeans 3D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image., supported parameters are: .P .RS 14 .I c = 3; int in [2, inf) .RS 2 number of classes. .RE .RE .TP 10 .B label A filter to label the connected components of a binary image., supported parameters are: .P .RS 14 .I n = 6n; factory .RS 2 neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .TP 10 .B labelmap Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: .P .RS 14 .I map =(required, input, string) .RS 2 Label mapping file. .RE .RE .TP 10 .B labelscale A filter that only creates output voxels that are already created in the input image. Scaling is done by using a voting algorithms that selects the target pixel value based on the highest pixel count of a certain label in the corresponding source region. If the region comprises two labels with the same count, the one with the lower number wins., supported parameters are: .P .RS 14 .I out-size =(required, 3dbounds) .RS 2 target size given as two coma separated values. .RE .RE .TP 10 .B load Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: .P .RS 14 .I file =(required, input, io) .RS 2 name of the input file to load from.. For supported file types see PLUGINS:3dimage/io .RE .RE .TP 10 .B lvdownscale This is a label voting downscale filter. It adownscales a 3D image by blocks. For each block the (non-zero) label that appears most times in the block is issued as output pixel in the target image. If two labels appear the same number of times, the one with the lower absolute value wins., supported parameters are: .P .RS 14 .I b = [[1,1,1]]; 3dbounds .RS 2 blocksize for the downscaling. Each block will be represented by one pixel in the target image.. .RE .RE .TP 10 .B mask Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: .P .RS 14 .I input =(required, input, io) .RS 2 second input image file name. For supported file types see PLUGINS:3dimage/io .RE .RE .TP 10 .B mean 3D image mean filter, supported parameters are: .P .RS 14 .I w = 1; int in [1, inf) .RS 2 half filter width. .RE .RE .TP 10 .B median median 3d filter, supported parameters are: .P .RS 14 .I w = 1; int in [1, inf) .RS 2 filter width parameter. .RE .RE .TP 10 .B mlv Mean of Least Variance 3D image filter, supported parameters are: .P .RS 14 .I w = 1; int in [1, inf) .RS 2 filter width parameter. .RE .RE .TP 10 .B msnormalizer 3D image mean-sigma normalizing filter, supported parameters are: .P .RS 14 .I w = 1; int in [1, inf) .RS 2 half filter width. .RE .RE .TP 10 .B open morphological open, supported parameters are: .P .RS 14 .I hint = black; string .RS 2 a hint at the main image content (black|white). .RE .RE .RS 14 .I shape = [sphere:r=2]; factory .RS 2 structuring element. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .TP 10 .B reorient 3D image reorientation filter, supported parameters are: .P .RS 14 .I map = xyz; dict .RS 2 oriantation mapping to be applied. Supported values are: .RS 4 .I xyz \(hy keep orientation .RE .RS 4 .I p\-yzx \(hy permutate x->z->y->x .RE .RS 4 .I p\-zxy \(hy permutate x->y->z->x .RE .RS 4 .I f\-yz \(hy flip y-z .RE .RS 4 .I f\-xy \(hy flip x-y .RE .RS 4 .I f\-xz \(hy flip x-z .RE .RS 4 .I r\-x90 \(hy rotate around x-axis clockwise 90 degree .RE .RS 4 .I r\-x180 \(hy rotate around x-axis clockwise 180 degree .RE .RS 4 .I r\-x270 \(hy rotate around x-axis clockwise 270 degree .RE .RS 4 .I r\-y90 \(hy rotate around y-axis clockwise 90 degree .RE .RS 4 .I r\-y180 \(hy rotate around y-axis clockwise 180 degree .RE .RS 4 .I r\-y270 \(hy rotate around y-axis clockwise 270 degree .RE .RS 4 .I r\-z90 \(hy rotate around z-axis clockwise 90 degree .RE .RS 4 .I r\-z180 \(hy rotate around z-axis clockwise 180 degree .RE .RS 4 .I r\-z270 \(hy rotate around z-axis clockwise 270 degree .RE .RE .RE .TP 10 .B resize Resize an image. The original data is centered within the new sized image., supported parameters are: .P .RS 14 .I size = [[0,0,0]]; streamable .RS 2 new size of the image a size 0 indicates to keep the size for the corresponding dimension.. .RE .RE .TP 10 .B sandp salt and pepper 3d filter, supported parameters are: .P .RS 14 .I thresh = 100; float in [0, inf) .RS 2 thresh value. .RE .RE .RS 14 .I w = 1; int in [1, inf) .RS 2 filter width parameter. .RE .RE .TP 10 .B scale 3D image filter that scales to a given target size , supported parameters are: .P .RS 14 .I interp = [bspline:d=3]; factory .RS 2 interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I s = [[0,0,0]]; 3dbounds .RS 2 target size to set all components at once (component 0:use input image size). .RE .RE .RS 14 .I sx = 0; uint in [0, inf) .RS 2 target size in x direction (0:use input image size). .RE .RE .RS 14 .I sy = 0; uint in [0, inf) .RS 2 target size in y direction (0:use input image size). .RE .RE .RS 14 .I sz = 0; uint in [0, inf) .RS 2 target size in y direction (0:use input image size). .RE .RE .TP 10 .B scharr The 3D Scharr filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable., supported parameters are: .P .RS 14 .I dir = x; dict .RS 2 Gradient direction. Supported values are: .RS 4 .I x \(hy gradient in x-direction .RE .RS 4 .I y \(hy gradient in y-direction .RE .RS 4 .I z \(hy gradient in z-direction .RE .RE .RE .TP 10 .B selectbig A filter that creats a binary mask representing the intensity with the highest pixel count.The pixel value 0 will be ignored, and if two intensities have the same pixel count, then the result is undefined. The input pixel must have an integral pixel type. .P .RS 14 (no parameters) .RE .TP 10 .B sepconv 3D image intensity separaple convolution filter, supported parameters are: .P .RS 14 .I kx = [gauss:w=1]; factory .RS 2 filter kernel in x\-direction. For supported plug-ins see PLUGINS:1d/spacialkernel .RE .RE .RS 14 .I ky = [gauss:w=1]; factory .RS 2 filter kernel in y\-direction. For supported plug-ins see PLUGINS:1d/spacialkernel .RE .RE .RS 14 .I kz = [gauss:w=1]; factory .RS 2 filter kernel in z\-direction. For supported plug-ins see PLUGINS:1d/spacialkernel .RE .RE .TP 10 .B sobel The 2D Sobel filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable., supported parameters are: .P .RS 14 .I dir = x; dict .RS 2 Gradient direction. Supported values are: .RS 4 .I x \(hy gradient in x-direction .RE .RS 4 .I y \(hy gradient in y-direction .RE .RS 4 .I z \(hy gradient in z-direction .RE .RE .RE .TP 10 .B sws seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image., supported parameters are: .P .RS 14 .I grad = 0; bool .RS 2 Interpret the input image as gradient. . .RE .RE .RS 14 .I mark = 0; bool .RS 2 Mark the segmented watersheds with a special gray scale value. .RE .RE .RS 14 .I n = [sphere:r=1]; factory .RS 2 Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .RS 14 .I seed =(required, input, string) .RS 2 seed input image containing the lables for the initial regions. .RE .RE .TP 10 .B tee Save the input image to a file and also pass it through to the next filter, supported parameters are: .P .RS 14 .I file =(required, output, io) .RS 2 name of the output file to save the image too.. For supported file types see PLUGINS:3dimage/io .RE .RE .TP 10 .B thinning 3D morphological thinning, based on: Lee and Kashyap, 'Building Skeleton Models via 3-D Medial Surface/Axis Thinning Algorithms', Graphical Models and Image Processing, 56(6):462-478, 1994. This implementation only supports the 26 neighbourhood. .P .RS 14 (no parameters) .RE .TP 10 .B transform Transform the input image with the given transformation., supported parameters are: .P .RS 14 .I file =(required, input, io) .RS 2 Name of the file containing the transformation.. For supported file types see PLUGINS:3dtransform/io .RE .RE .RS 14 .I imgboundary = ; factory .RS 2 override image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = ; factory .RS 2 override image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .TP 10 .B variance 3D image variance filter, supported parameters are: .P .RS 14 .I w = 1; int in [1, inf) .RS 2 half filter width. .RE .RE .TP 10 .B ws basic watershead segmentation., supported parameters are: .P .RS 14 .I evalgrad = 0; bool .RS 2 Set to 1 if the input image does not represent a gradient norm image. .RE .RE .RS 14 .I mark = 0; bool .RS 2 Mark the segmented watersheds with a special gray scale value. .RE .RE .RS 14 .I n = [sphere:r=1]; factory .RS 2 Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape .RE .RE .RS 14 .I thresh = 0; float in [0, 1) .RS 2 Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad \- min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined. .RE .RE .SH PLUGINS: 3dimage/fullcost .TP 10 .B image Generalized image similarity cost function that also handles multi-resolution processing. The actual similarity measure is given es extra parameter., supported parameters are: .P .RS 14 .I cost = ssd; factory .RS 2 Cost function kernel. For supported plug-ins see PLUGINS:3dimage/cost .RE .RE .RS 14 .I debug = 0; bool .RS 2 Save intermediate resuts for debugging. .RE .RE .RS 14 .I ref =(input, io) .RS 2 Reference image. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I src =(input, io) .RS 2 Study image. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I weight = 1; float .RS 2 weight of cost function. .RE .RE .TP 10 .B labelimage Similarity cost function that maps labels of two images and handles label-preserving multi-resolution processing., supported parameters are: .P .RS 14 .I maxlabel = 256; int in [2, 32000] .RS 2 maximum number of labels to consider. .RE .RE .RS 14 .I ref =(input, io) .RS 2 Reference image. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I src =(input, io) .RS 2 Study image. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I weight = 1; float .RS 2 weight of cost function. .RE .RE .TP 10 .B maskedimage Generalized masked image similarity cost function that also handles multi-resolution processing. The provided masks should be densly filled regions in multi-resolution procesing because otherwise the mask information may get lost when downscaling the image. The mask may be pre-filtered - after pre-filtering the masks must be of bit-type.The reference mask and the transformed mask of the study image are combined by binary AND. The actual similarity measure is given es extra parameter., supported parameters are: .P .RS 14 .I cost = ssd; factory .RS 2 Cost function kernel. For supported plug-ins see PLUGINS:3dimage/maskedcost .RE .RE .RS 14 .I ref =(input, io) .RS 2 Reference image. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I ref-mask =(input, io) .RS 2 Reference image mask (binary). For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I ref-mask-filter = ; factory .RS 2 Filter to prepare the reference mask image, the output must be a binary image.. For supported plug-ins see PLUGINS:3dimage/filter .RE .RE .RS 14 .I src =(input, io) .RS 2 Study image. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I src-mask =(input, io) .RS 2 Study image mask (binary). For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I src-mask-filter = ; factory .RS 2 Filter to prepare the study mask image, the output must be a binary image.. For supported plug-ins see PLUGINS:3dimage/filter .RE .RE .RS 14 .I weight = 1; float .RS 2 weight of cost function. .RE .RE .TP 10 .B taggedssd Evaluates the Sum of Squared Differences similarity measure by using three tagged image pairs. The cost function value is evaluated based on all image pairs, but the gradient is composed by composing its component based on the tag direction., supported parameters are: .P .RS 14 .I refx =(input, io) .RS 2 Reference image X\-tag. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I refy =(input, io) .RS 2 Reference image Y\-tag. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I refz =(input, io) .RS 2 Reference image Z\-tag. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I srcx =(input, io) .RS 2 Study image X\-tag. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I srcy =(input, io) .RS 2 Study image Y\-tag. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I srcz =(input, io) .RS 2 Study image Z\-tag. For supported file types see PLUGINS:3dimage/io .RE .RE .RS 14 .I weight = 1; float .RS 2 weight of cost function. .RE .RE .SH PLUGINS: 3dimage/io .TP 10 .B analyze Analyze 7.5 image .P .RS 14 Recognized file extensions: .HDR, .hdr .RE .RS 14 Supported element types: .RS 2 unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B datapool Virtual IO to and from the internal data pool .P .RS 14 Recognized file extensions: .@ .RE .TP 10 .B dicom Dicom image series as 3D .P .RS 14 Recognized file extensions: .DCM, .dcm .RE .RS 14 Supported element types: .RS 2 signed 16 bit, unsigned 16 bit .RE .RE .TP 10 .B hdf5 HDF5 3D image IO .P .RS 14 Recognized file extensions: .H5, .h5 .RE .RS 14 Supported element types: .RS 2 binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B inria INRIA image .P .RS 14 Recognized file extensions: .INR, .inr .RE .RS 14 Supported element types: .RS 2 signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B mhd MetaIO 3D image IO using the VTK implementation (experimental). .P .RS 14 Recognized file extensions: .MHA, .MHD, .mha, .mhd .RE .RS 14 Supported element types: .RS 2 signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B nifti NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package. .P .RS 14 Recognized file extensions: .NII, .nii .RE .RS 14 Supported element types: .RS 2 signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B vff VFF Sun raster format .P .RS 14 Recognized file extensions: .VFF, .vff .RE .RS 14 Supported element types: .RS 2 unsigned 8 bit, signed 16 bit .RE .RE .TP 10 .B vista Vista 3D .P .RS 14 Recognized file extensions: .-, .V, .VISTA, .v, .vista .RE .RS 14 Supported element types: .RS 2 binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B vti 3D image VTK-XML in- and output (experimental). .P .RS 14 Recognized file extensions: .VTI, .vti .RE .RS 14 Supported element types: .RS 2 signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .TP 10 .B vtk 3D VTK image legacy in- and output (experimental). .P .RS 14 Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage .RE .RS 14 Supported element types: .RS 2 signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64 bit .RE .RE .SH PLUGINS: 3dimage/maskedcost .TP 10 .B lncc local normalized cross correlation with masking support., supported parameters are: .P .RS 14 .I w = 5; uint in [1, 256] .RS 2 half width of the window used for evaluating the localized cross correlation. .RE .RE .TP 10 .B mi Spline parzen based mutual information with masking., supported parameters are: .P .RS 14 .I cut = 0; float in [0, 40] .RS 2 Percentage of pixels to cut at high and low intensities to remove outliers. .RE .RE .RS 14 .I mbins = 64; uint in [1, 256] .RS 2 Number of histogram bins used for the moving image. .RE .RE .RS 14 .I mkernel = [bspline:d=3]; factory .RS 2 Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I rbins = 64; uint in [1, 256] .RS 2 Number of histogram bins used for the reference image. .RE .RE .RS 14 .I rkernel = [bspline:d=0]; factory .RS 2 Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .TP 10 .B ncc normalized cross correlation with masking support. .P .RS 14 (no parameters) .RE .TP 10 .B ssd Sum of squared differences with masking. .P .RS 14 (no parameters) .RE .SH PLUGINS: 3dimage/shape .TP 10 .B 18n 18n neighborhood 3D shape creator .P .RS 14 (no parameters) .RE .TP 10 .B 26n 26n neighborhood 3D shape creator .P .RS 14 (no parameters) .RE .TP 10 .B 6n 6n neighborhood 3D shape creator .P .RS 14 (no parameters) .RE .TP 10 .B sphere Closed spherical shape neighborhood including the pixels within a given radius r., supported parameters are: .P .RS 14 .I r = 2; float in (0, inf) .RS 2 sphere radius. .RE .RE .SH PLUGINS: 3dimage/transform .TP 10 .B affine Affine transformation (12 degrees of freedom), supported parameters are: .P .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .TP 10 .B axisrot Restricted rotation transformation (1 degrees of freedom). The transformation is restricted to the rotation around the given axis about the given rotation center, supported parameters are: .P .RS 14 .I axis =(required, 3dfvector) .RS 2 rotation axis. .RE .RE .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I origin =(required, 3dfvector) .RS 2 center of the transformation. .RE .RE .TP 10 .B raffine Restricted affine transformation (3 degrees of freedom). The transformation is restricted to the rotation around the given axis and shearing along the two axis perpendicular to the given one, supported parameters are: .P .RS 14 .I axis =(required, 3dfvector) .RS 2 rotation axis. .RE .RE .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I origin =(required, 3dfvector) .RS 2 center of the transformation. .RE .RE .TP 10 .B rigid Rigid transformation, i.e. rotation and translation (six degrees of freedom)., supported parameters are: .P .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I origin = [[0,0,0]]; 3dfvector .RS 2 Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of the volume. .RE .RE .TP 10 .B rotation Rotation transformation (three degrees of freedom)., supported parameters are: .P .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I origin = [[0,0,0]]; 3dfvector .RS 2 Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of the volume. .RE .RE .TP 10 .B rotbend Restricted transformation (4 degrees of freedom). The transformation is restricted to the rotation around the x and y axis and a bending along the x axis, independedn in each direction, with the bending increasing with the squared distance from the rotation axis., supported parameters are: .P .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I norot = 0; bool .RS 2 Don't optimize the rotation. .RE .RE .RS 14 .I origin =(required, 3dfvector) .RS 2 center of the transformation. .RE .RE .TP 10 .B spline Free-form transformation that can be described by a set of B-spline coefficients and an underlying B-spline kernel., supported parameters are: .P .RS 14 .I anisorate = [[0,0,0]]; 3dfvector .RS 2 anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value.. .RE .RE .RS 14 .I debug = 0; bool .RS 2 enable additional debugging output. .RE .RE .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I kernel = [bspline:d=3]; factory .RS 2 transformation spline kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .RS 14 .I penalty = ; factory .RS 2 transformation penalty energy term. For supported plug-ins see PLUGINS:3dtransform/splinepenalty .RE .RE .RS 14 .I rate = 10; float in [1, inf) .RS 2 isotropic coefficient rate in pixels. .RE .RE .TP 10 .B translate Translation (three degrees of freedom), supported parameters are: .P .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .TP 10 .B vf This plug-in implements a transformation that defines a translation for each point of the grid defining the domain of the transformation., supported parameters are: .P .RS 14 .I imgboundary = mirror; factory .RS 2 image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc .RE .RE .RS 14 .I imgkernel = [bspline:d=3]; factory .RS 2 image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel .RE .RE .SH PLUGINS: 3dtransform/io .TP 10 .B bbs Binary (non-portable) serialized IO of 3D transformations .P .RS 14 Recognized file extensions: .bbs .RE .TP 10 .B datapool Virtual IO to and from the internal data pool .P .RS 14 Recognized file extensions: .@ .RE .TP 10 .B vista Vista storage of 3D transformations .P .RS 14 Recognized file extensions: .v, .v3dt .RE .TP 10 .B xml XML serialized IO of 3D transformations .P .RS 14 Recognized file extensions: .x3dt .RE .SH PLUGINS: 3dtransform/splinepenalty .TP 10 .B divcurl divcurl penalty on the transformation, supported parameters are: .P .RS 14 .I curl = 1; float in [0, inf) .RS 2 penalty weight on curl. .RE .RE .RS 14 .I div = 1; float in [0, inf) .RS 2 penalty weight on divergence. .RE .RE .RS 14 .I norm = 0; bool .RS 2 Set to 1 if the penalty should be normalized with respect to the image size. .RE .RE .RS 14 .I weight = 1; float in (0, inf) .RS 2 weight of penalty energy. .RE .RE .SH PLUGINS: minimizer/singlecost .TP 10 .B gdas Gradient descent with automatic step size correction., supported parameters are: .P .RS 14 .I ftolr = 0; double in [0, inf) .RS 2 Stop if the relative change of the criterion is below.. .RE .RE .RS 14 .I max-step = 2; double in (0, inf) .RS 2 Maximal absolute step size. .RE .RE .RS 14 .I maxiter = 200; uint in [1, inf) .RS 2 Stopping criterion: the maximum number of iterations. .RE .RE .RS 14 .I min-step = 0.1; double in (0, inf) .RS 2 Minimal absolute step size. .RE .RE .RS 14 .I xtola = 0.01; double in [0, inf) .RS 2 Stop if the inf\-norm of the change applied to x is below this value.. .RE .RE .TP 10 .B gdsq Gradient descent with quadratic step estimation, supported parameters are: .P .RS 14 .I ftolr = 0; double in [0, inf) .RS 2 Stop if the relative change of the criterion is below.. .RE .RE .RS 14 .I gtola = 0; double in [0, inf) .RS 2 Stop if the inf\-norm of the gradient is below this value.. .RE .RE .RS 14 .I maxiter = 100; uint in [1, inf) .RS 2 Stopping criterion: the maximum number of iterations. .RE .RE .RS 14 .I scale = 2; double in (1, inf) .RS 2 Fallback fixed step size scaling. .RE .RE .RS 14 .I step = 0.1; double in (0, inf) .RS 2 Initial step size. .RE .RE .RS 14 .I xtola = 0; double in [0, inf) .RS 2 Stop if the inf\-norm of x\-update is below this value.. .RE .RE .TP 10 .B gsl optimizer plugin based on the multimin optimizers of the GNU Scientific Library (GSL) https://www.gnu.org/software/gsl/, supported parameters are: .P .RS 14 .I eps = 0.01; double in (0, inf) .RS 2 gradient based optimizers: stop when |grad| < eps, simplex: stop when simplex size < eps.. .RE .RE .RS 14 .I iter = 100; uint in [1, inf) .RS 2 maximum number of iterations. .RE .RE .RS 14 .I opt = gd; dict .RS 2 Specific optimizer to be used.. Supported values are: .RS 4 .I simplex \(hy Simplex algorithm of Nelder and Mead .RE .RS 4 .I cg\-fr \(hy Flecher-Reeves conjugate gradient algorithm .RE .RS 4 .I cg\-pr \(hy Polak-Ribiere conjugate gradient algorithm .RE .RS 4 .I bfgs \(hy Broyden-Fletcher-Goldfarb-Shann .RE .RS 4 .I bfgs2 \(hy Broyden-Fletcher-Goldfarb-Shann (most efficient version) .RE .RS 4 .I gd \(hy Gradient descent. .RE .RE .RE .RS 14 .I step = 0.001; double in (0, inf) .RS 2 initial step size. .RE .RE .RS 14 .I tol = 0.1; double in (0, inf) .RS 2 some tolerance parameter. .RE .RE .TP 10 .B nlopt Minimizer algorithms using the NLOPT library, for a description of the optimizers please see 'http://ab-initio.mit.edu/wiki/index.php/NLopt_Algorithms', supported parameters are: .P .RS 14 .I ftola = 0; double in [0, inf) .RS 2 Stopping criterion: the absolute change of the objective value is below this value. .RE .RE .RS 14 .I ftolr = 0; double in [0, inf) .RS 2 Stopping criterion: the relative change of the objective value is below this value. .RE .RE .RS 14 .I higher = inf; double .RS 2 Higher boundary (equal for all parameters). .RE .RE .RS 14 .I local-opt = none; dict .RS 2 local minimization algorithm that may be required for the main minimization algorithm.. Supported values are: .RS 4 .I gn\-direct \(hy Dividing Rectangles .RE .RS 4 .I gn\-direct\-l \(hy Dividing Rectangles (locally biased) .RE .RS 4 .I gn\-direct\-l\-rand \(hy Dividing Rectangles (locally biased, randomized) .RE .RS 4 .I gn\-direct\-noscal \(hy Dividing Rectangles (unscaled) .RE .RS 4 .I gn\-direct\-l\-noscal \(hy Dividing Rectangles (unscaled, locally biased) .RE .RS 4 .I gn\-direct\-l\-rand\-noscale \(hy Dividing Rectangles (unscaled, locally biased, randomized) .RE .RS 4 .I gn\-orig\-direct \(hy Dividing Rectangles (original implementation) .RE .RS 4 .I gn\-orig\-direct\-l \(hy Dividing Rectangles (original implementation, locally biased) .RE .RS 4 .I ld\-lbfgs\-nocedal \(hy None .RE .RS 4 .I ld\-lbfgs \(hy Low-storage BFGS .RE .RS 4 .I ln\-praxis \(hy Gradient-free Local Optimization via the Principal-Axis Method .RE .RS 4 .I ld\-var1 \(hy Shifted Limited-Memory Variable-Metric, Rank 1 .RE .RS 4 .I ld\-var2 \(hy Shifted Limited-Memory Variable-Metric, Rank 2 .RE .RS 4 .I ld\-tnewton \(hy Truncated Newton .RE .RS 4 .I ld\-tnewton\-restart \(hy Truncated Newton with steepest-descent restarting .RE .RS 4 .I ld\-tnewton\-precond \(hy Preconditioned Truncated Newton .RE .RS 4 .I ld\-tnewton\-precond\-restart \(hy Preconditioned Truncated Newton with steepest-descent restarting .RE .RS 4 .I gn\-crs2\-lm \(hy Controlled Random Search with Local Mutation .RE .RS 4 .I ld\-mma \(hy Method of Moving Asymptotes .RE .RS 4 .I ln\-cobyla \(hy Constrained Optimization BY Linear Approximation .RE .RS 4 .I ln\-newuoa \(hy Derivative-free Unconstrained Optimization by Iteratively Constructed Quadratic Approximation .RE .RS 4 .I ln\-newuoa\-bound \(hy Derivative-free Bound-constrained Optimization by Iteratively Constructed Quadratic Approximation .RE .RS 4 .I ln\-neldermead \(hy Nelder-Mead simplex algorithm .RE .RS 4 .I ln\-sbplx \(hy Subplex variant of Nelder-Mead .RE .RS 4 .I ln\-bobyqa \(hy Derivative-free Bound-constrained Optimization .RE .RS 4 .I gn\-isres \(hy Improved Stochastic Ranking Evolution Strategy .RE .RS 4 .I none \(hy don't specify algorithm .RE .RE .RE .RS 14 .I lower = \-inf; double .RS 2 Lower boundary (equal for all parameters). .RE .RE .RS 14 .I maxiter = 100; int in [1, inf) .RS 2 Stopping criterion: the maximum number of iterations. .RE .RE .RS 14 .I opt = ld\-lbfgs; dict .RS 2 main minimization algorithm. Supported values are: .RS 4 .I gn\-direct \(hy Dividing Rectangles .RE .RS 4 .I gn\-direct\-l \(hy Dividing Rectangles (locally biased) .RE .RS 4 .I gn\-direct\-l\-rand \(hy Dividing Rectangles (locally biased, randomized) .RE .RS 4 .I gn\-direct\-noscal \(hy Dividing Rectangles (unscaled) .RE .RS 4 .I gn\-direct\-l\-noscal \(hy Dividing Rectangles (unscaled, locally biased) .RE .RS 4 .I gn\-direct\-l\-rand\-noscale \(hy Dividing Rectangles (unscaled, locally biased, randomized) .RE .RS 4 .I gn\-orig\-direct \(hy Dividing Rectangles (original implementation) .RE .RS 4 .I gn\-orig\-direct\-l \(hy Dividing Rectangles (original implementation, locally biased) .RE .RS 4 .I ld\-lbfgs\-nocedal \(hy None .RE .RS 4 .I ld\-lbfgs \(hy Low-storage BFGS .RE .RS 4 .I ln\-praxis \(hy Gradient-free Local Optimization via the Principal-Axis Method .RE .RS 4 .I ld\-var1 \(hy Shifted Limited-Memory Variable-Metric, Rank 1 .RE .RS 4 .I ld\-var2 \(hy Shifted Limited-Memory Variable-Metric, Rank 2 .RE .RS 4 .I ld\-tnewton \(hy Truncated Newton .RE .RS 4 .I ld\-tnewton\-restart \(hy Truncated Newton with steepest-descent restarting .RE .RS 4 .I ld\-tnewton\-precond \(hy Preconditioned Truncated Newton .RE .RS 4 .I ld\-tnewton\-precond\-restart \(hy Preconditioned Truncated Newton with steepest-descent restarting .RE .RS 4 .I gn\-crs2\-lm \(hy Controlled Random Search with Local Mutation .RE .RS 4 .I ld\-mma \(hy Method of Moving Asymptotes .RE .RS 4 .I ln\-cobyla \(hy Constrained Optimization BY Linear Approximation .RE .RS 4 .I ln\-newuoa \(hy Derivative-free Unconstrained Optimization by Iteratively Constructed Quadratic Approximation .RE .RS 4 .I ln\-newuoa\-bound \(hy Derivative-free Bound-constrained Optimization by Iteratively Constructed Quadratic Approximation .RE .RS 4 .I ln\-neldermead \(hy Nelder-Mead simplex algorithm .RE .RS 4 .I ln\-sbplx \(hy Subplex variant of Nelder-Mead .RE .RS 4 .I ln\-bobyqa \(hy Derivative-free Bound-constrained Optimization .RE .RS 4 .I gn\-isres \(hy Improved Stochastic Ranking Evolution Strategy .RE .RS 4 .I auglag \(hy Augmented Lagrangian algorithm .RE .RS 4 .I auglag\-eq \(hy Augmented Lagrangian algorithm with equality constraints only .RE .RS 4 .I g\-mlsl \(hy Multi-Level Single-Linkage (require local optimization and bounds) .RE .RS 4 .I g\-mlsl\-lds \(hy Multi-Level Single-Linkage (low-discrepancy-sequence, require local gradient based optimization and bounds) .RE .RS 4 .I ld\-slsqp \(hy Sequential Least-Squares Quadratic Programming .RE .RE .RE .RS 14 .I step = 0; double in [0, inf) .RS 2 Initial step size for gradient free methods. .RE .RE .RS 14 .I stop = \-inf; double .RS 2 Stopping criterion: function value falls below this value. .RE .RE .RS 14 .I xtola = 0; double in [0, inf) .RS 2 Stopping criterion: the absolute change of all x\-values is below this value. .RE .RE .RS 14 .I xtolr = 0; double in [0, inf) .RS 2 Stopping criterion: the relative change of all x\-values is below this value. .RE .RE .SH EXAMPLE Run a serial registration of images inputXXXX.v (X digit) to reference image 20 and store the result in regXXXX.v. Optimize the sum of squared differences and spline transformations with coefficient rate 10. .HP mia\-3dserial\-nonrigid \-i input0000.v \-o 'reg%04d.v' \-f spline:rate=10 \-r 20 ssd .SH AUTHOR(s) Gert Wollny .SH COPYRIGHT This software is Copyright (c) 1999\(hy2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option '\-\-copyright'.