--- name: "mia-3dcost" section: "1" platform: "linux" package: "mia-tools" version: "2.4.7-11+b1" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/mia-3dcost" --- # mia-3dcost(1) Evaluate similarity of two 3D images. ## NAME mia-3dcost - Evaluate similarity of two 3D images. ## SYNOPSIS **mia-3dcost \[options\] \** ## DESCRIPTION **mia-3dcost** This program evauates the cost function as given by the free parameters on the command line. ## OPTIONS ### Help & Info - \-V --verbose=warning verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: *trace* ‐ Function call trace *debug* ‐ Debug output *info* ‐ Low level messages *message* ‐ Normal messages *warning* ‐ Warnings *fail* ‐ Report test failures *error* ‐ Report errors *fatal* ‐ Report only fatal errors - \--copyright print copyright information - \-h --help print this help - \-? --usage print a short help - \--version print the version number and exit ### Processing - \--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). ## PLUGINS: 1d/spacialkernel - **cdiff** Central difference filter kernel, mirror boundary conditions are used. (no parameters) - **gauss** spacial Gauss filter kernel, supported parameters are: *w* = 1; uint in \[0, inf) half filter width. - **scharr** This plugin provides the 1D folding kernel for the Scharr gradient filter (no parameters) ## PLUGINS: 1d/splinebc - **mirror** Spline interpolation boundary conditions that mirror on the boundary (no parameters) - **repeat** Spline interpolation boundary conditions that repeats the value at the boundary (no parameters) - **zero** Spline interpolation boundary conditions that assumes zero for values outside (no parameters) ## PLUGINS: 1d/splinekernel - **bspline** B-spline kernel creation , supported parameters are: *d* = 3; int in \[0, 5\] Spline degree. - **omoms** OMoms-spline kernel creation, supported parameters are: *d* = 3; int in \[3, 3\] Spline degree. ## PLUGINS: 3dimage/combiner - **absdiff** Image combiner 'absdiff' (no parameters) - **add** Image combiner 'add' (no parameters) - **div** Image combiner 'div' (no parameters) - **mul** Image combiner 'mul' (no parameters) - **sub** Image combiner 'sub' (no parameters) ## PLUGINS: 3dimage/cost - **lncc** local normalized cross correlation with masking support., supported parameters are: *w* = 5; uint in \[1, 256\] half width of the window used for evaluating the localized cross correlation. - **mi** Spline parzen based mutual information., supported parameters are: *cut* = 0; float in \[0, 40\] Percentage of pixels to cut at high and low intensities to remove outliers. *mbins* = 64; uint in \[1, 256\] Number of histogram bins used for the moving image. *mkernel* = \[bspline:d=3\]; factory Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel *rbins* = 64; uint in \[1, 256\] Number of histogram bins used for the reference image. *rkernel* = \[bspline:d=0\]; factory Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel - **ncc** normalized cross correlation. (no parameters) - **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: *eval* = ds; dict plugin subtype (sq, ds,dot,cross). Supported values are: *ds* ‐ square of scaled difference *dot* ‐ scalar product kernel *cross* ‐ cross product kernel - **ssd** 3D image cost: sum of squared differences, supported parameters are: *autothresh* = 0; float in \[0, 1000\] Use automatic masking of the moving image by only takeing intensity values into accound that are larger than the given threshold. *norm* = 0; bool Set whether the metric should be normalized by the number of image pixels. - **ssd-automask** 3D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are: *rthresh* = 0; double Threshold intensity value for reference image. *sthresh* = 0; double Threshold intensity value for source image. ## PLUGINS: 3dimage/filter - **bandpass** intensity bandpass filter, supported parameters are: *max* = 3.40282e+38; float maximum of the band. *min* = 0; float minimum of the band. - **binarize** image binarize filter, supported parameters are: *max* = 3.40282e+38; float maximum of accepted range. *min* = 0; float minimum of accepted range. - **close** morphological close, supported parameters are: *hint* = black; string a hint at the main image content (black\|white). *shape* = \[sphere:r=2\]; factory structuring element. For supported plug-ins see PLUGINS:3dimage/shape - **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: *image* =(required, input, io) second image that is needed in the combiner. For supported file types see PLUGINS:3dimage/io *op* =(required, factory) Image combiner to be applied to the images. For supported plug-ins see PLUGINS:3dimage/combiner *reverse* = 0; bool reverse the order in which the images passed to the combiner. - **convert** image pixel format conversion filter, supported parameters are: *a* = 1; float linear conversion parameter a. *b* = 0; float linear conversion parameter b. *map* = opt; dict conversion mapping. Supported values are: *copy* ‐ copy data when converting *linear* ‐ apply linear transformation x -\> a\*x+b *range* ‐ apply linear transformation that maps the input data type range to the output data type range *opt* ‐ apply a linear transformation that maps the real input range to the full output range *optstat* ‐ apply a linear transform that maps based on input mean and variation to the full output range *repn* = ubyte; dict output pixel type. Supported values are: *bit* ‐ binary data *sbyte* ‐ signed 8 bit *ubyte* ‐ unsigned 8 bit *sshort* ‐ signed 16 bit *ushort* ‐ unsigned 16 bit *sint* ‐ signed 32 bit *uint* ‐ unsigned 32 bit *slong* ‐ signed 64 bit *ulong* ‐ unsigned 64 bit *float* ‐ floating point 32 bit *double* ‐ floating point 64 bit *none* ‐ no pixel type defined - **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: *end* = \[\[4294967295,4294967295,4294967295\]\]; streamable end of cropping range, maximum = (-1,-1,-1). *start* = \[\[0,0,0\]\]; streamable begin of cropping range. - **dilate** 3d image stack dilate filter, supported parameters are: *hint* = black; string a hint at the main image content (black\|white). *shape* = \[sphere:r=2\]; factory structuring element. For supported plug-ins see PLUGINS:3dimage/shape - **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. (no parameters) - **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: *b* = \[\[1,1,1\]\]; 3dbounds blocksize. *bx* = 1; uint in \[1, inf) blocksize in x direction. *by* = 1; uint in \[1, inf) blocksize in y direction. *bz* = 1; uint in \[1, inf) blocksize in z direction. *kernel* = gauss; factory 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 - **erode** 3d image stack erode filter, supported parameters are: *hint* = black; string a hint at the main image content (black\|white). *shape* = \[sphere:r=2\]; factory structuring element. For supported plug-ins see PLUGINS:3dimage/shape - **gauss** isotropic 3D gauss filter, supported parameters are: *w* = 1; int in \[0, inf) filter width parameter. - **gradnorm** 3D image to gradient norm filter (no parameters) - **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: *min* = 1; float lower threshold for mask growing. *ref* =(required, input, io) reference image for mask region growing. For supported file types see PLUGINS:3dimage/io *shape* = 6n; factory neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape - **invert** intensity invert filter (no parameters) - **isovoxel** This filter scales an image to make the voxel size isometric and its size to correspond to the given value, supported parameters are: *interp* = \[bspline:d=3\]; factory interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel *size* = 1; float in (0, inf) isometric target voxel size. - **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: *c* = 3; int in \[2, inf) number of classes. - **label** A filter to label the connected components of a binary image., supported parameters are: *n* = 6n; factory neighborhood mask. For supported plug-ins see PLUGINS:3dimage/shape - **labelmap** Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: *map* =(required, input, string) Label mapping file. - **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: *out-size* =(required, 3dbounds) target size given as two coma separated values. - **load** Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: *file* =(required, input, io) name of the input file to load from.. For supported file types see PLUGINS:3dimage/io - **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: *b* = \[\[1,1,1\]\]; 3dbounds blocksize for the downscaling. Each block will be represented by one pixel in the target image.. - **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: *input* =(required, input, io) second input image file name. For supported file types see PLUGINS:3dimage/io - **mean** 3D image mean filter, supported parameters are: *w* = 1; int in \[1, inf) half filter width. - **median** median 3d filter, supported parameters are: *w* = 1; int in \[1, inf) filter width parameter. - **mlv** Mean of Least Variance 3D image filter, supported parameters are: *w* = 1; int in \[1, inf) filter width parameter. - **msnormalizer** 3D image mean-sigma normalizing filter, supported parameters are: *w* = 1; int in \[1, inf) half filter width. - **open** morphological open, supported parameters are: *hint* = black; string a hint at the main image content (black\|white). *shape* = \[sphere:r=2\]; factory structuring element. For supported plug-ins see PLUGINS:3dimage/shape - **reorient** 3D image reorientation filter, supported parameters are: *map* = xyz; dict oriantation mapping to be applied. Supported values are: *xyz* ‐ keep orientation *p-yzx* ‐ permutate x-\>z-\>y-\>x *p-zxy* ‐ permutate x-\>y-\>z-\>x *f-yz* ‐ flip y-z *f-xy* ‐ flip x-y *f-xz* ‐ flip x-z *r-x90* ‐ rotate around x-axis clockwise 90 degree *r-x180* ‐ rotate around x-axis clockwise 180 degree *r-x270* ‐ rotate around x-axis clockwise 270 degree *r-y90* ‐ rotate around y-axis clockwise 90 degree *r-y180* ‐ rotate around y-axis clockwise 180 degree *r-y270* ‐ rotate around y-axis clockwise 270 degree *r-z90* ‐ rotate around z-axis clockwise 90 degree *r-z180* ‐ rotate around z-axis clockwise 180 degree *r-z270* ‐ rotate around z-axis clockwise 270 degree - **resize** Resize an image. The original data is centered within the new sized image., supported parameters are: *size* = \[\[0,0,0\]\]; streamable new size of the image a size 0 indicates to keep the size for the corresponding dimension.. - **sandp** salt and pepper 3d filter, supported parameters are: *thresh* = 100; float in \[0, inf) thresh value. *w* = 1; int in \[1, inf) filter width parameter. - **scale** 3D image filter that scales to a given target size , supported parameters are: *interp* = \[bspline:d=3\]; factory interpolation kernel to be used . For supported plug-ins see PLUGINS:1d/splinekernel *s* = \[\[0,0,0\]\]; 3dbounds target size to set all components at once (component 0:use input image size). *sx* = 0; uint in \[0, inf) target size in x direction (0:use input image size). *sy* = 0; uint in \[0, inf) target size in y direction (0:use input image size). *sz* = 0; uint in \[0, inf) target size in y direction (0:use input image size). - **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: *dir* = x; dict Gradient direction. Supported values are: *x* ‐ gradient in x-direction *y* ‐ gradient in y-direction *z* ‐ gradient in z-direction - **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. (no parameters) - **sepconv** 3D image intensity separaple convolution filter, supported parameters are: *kx* = \[gauss:w=1\]; factory filter kernel in x-direction. For supported plug-ins see PLUGINS:1d/spacialkernel *ky* = \[gauss:w=1\]; factory filter kernel in y-direction. For supported plug-ins see PLUGINS:1d/spacialkernel *kz* = \[gauss:w=1\]; factory filter kernel in z-direction. For supported plug-ins see PLUGINS:1d/spacialkernel - **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: *dir* = x; dict Gradient direction. Supported values are: *x* ‐ gradient in x-direction *y* ‐ gradient in y-direction *z* ‐ gradient in z-direction - **sws** seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image., supported parameters are: *grad* = 0; bool Interpret the input image as gradient. . *mark* = 0; bool Mark the segmented watersheds with a special gray scale value. *n* = \[sphere:r=1\]; factory Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape *seed* =(required, input, string) seed input image containing the lables for the initial regions. - **tee** Save the input image to a file and also pass it through to the next filter, supported parameters are: *file* =(required, output, io) name of the output file to save the image too.. For supported file types see PLUGINS:3dimage/io - **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. (no parameters) - **transform** Transform the input image with the given transformation., supported parameters are: *file* =(required, input, io) Name of the file containing the transformation.. For supported file types see PLUGINS:3dtransform/io *imgboundary* = ; factory override image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = ; factory override image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel - **variance** 3D image variance filter, supported parameters are: *w* = 1; int in \[1, inf) half filter width. - **ws** basic watershead segmentation., supported parameters are: *evalgrad* = 0; bool Set to 1 if the input image does not represent a gradient norm image. *mark* = 0; bool Mark the segmented watersheds with a special gray scale value. *n* = \[sphere:r=1\]; factory Neighborhood for watershead region growing. For supported plug-ins see PLUGINS:3dimage/shape *thresh* = 0; float in \[0, 1) 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. ## PLUGINS: 3dimage/fullcost - **image** Generalized image similarity cost function that also handles multi-resolution processing. The actual similarity measure is given es extra parameter., supported parameters are: *cost* = ssd; factory Cost function kernel. For supported plug-ins see PLUGINS:3dimage/cost *debug* = 0; bool Save intermediate resuts for debugging. *ref* =(input, io) Reference image. For supported file types see PLUGINS:3dimage/io *src* =(input, io) Study image. For supported file types see PLUGINS:3dimage/io *weight* = 1; float weight of cost function. - **labelimage** Similarity cost function that maps labels of two images and handles label-preserving multi-resolution processing., supported parameters are: *maxlabel* = 256; int in \[2, 32000\] maximum number of labels to consider. *ref* =(input, io) Reference image. For supported file types see PLUGINS:3dimage/io *src* =(input, io) Study image. For supported file types see PLUGINS:3dimage/io *weight* = 1; float weight of cost function. - **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: *cost* = ssd; factory Cost function kernel. For supported plug-ins see PLUGINS:3dimage/maskedcost *ref* =(input, io) Reference image. For supported file types see PLUGINS:3dimage/io *ref-mask* =(input, io) Reference image mask (binary). For supported file types see PLUGINS:3dimage/io *ref-mask-filter* = ; factory Filter to prepare the reference mask image, the output must be a binary image.. For supported plug-ins see PLUGINS:3dimage/filter *src* =(input, io) Study image. For supported file types see PLUGINS:3dimage/io *src-mask* =(input, io) Study image mask (binary). For supported file types see PLUGINS:3dimage/io *src-mask-filter* = ; factory Filter to prepare the study mask image, the output must be a binary image.. For supported plug-ins see PLUGINS:3dimage/filter *weight* = 1; float weight of cost function. - **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: *refx* =(input, io) Reference image X-tag. For supported file types see PLUGINS:3dimage/io *refy* =(input, io) Reference image Y-tag. For supported file types see PLUGINS:3dimage/io *refz* =(input, io) Reference image Z-tag. For supported file types see PLUGINS:3dimage/io *srcx* =(input, io) Study image X-tag. For supported file types see PLUGINS:3dimage/io *srcy* =(input, io) Study image Y-tag. For supported file types see PLUGINS:3dimage/io *srcz* =(input, io) Study image Z-tag. For supported file types see PLUGINS:3dimage/io *weight* = 1; float weight of cost function. ## PLUGINS: 3dimage/io - **analyze** Analyze 7.5 image Recognized file extensions: .HDR, .hdr Supported element types: unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64 bit - **datapool** Virtual IO to and from the internal data pool Recognized file extensions: .@ - **dicom** Dicom image series as 3D Recognized file extensions: .DCM, .dcm Supported element types: signed 16 bit, unsigned 16 bit - **hdf5** HDF5 3D image IO Recognized file extensions: .H5, .h5 Supported element types: 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 - **inria** INRIA image Recognized file extensions: .INR, .inr Supported element types: 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 - **mhd** MetaIO 3D image IO using the VTK implementation (experimental). Recognized file extensions: .MHA, .MHD, .mha, .mhd Supported element types: 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 - **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. Recognized file extensions: .NII, .nii Supported element types: 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 - **vff** VFF Sun raster format Recognized file extensions: .VFF, .vff Supported element types: unsigned 8 bit, signed 16 bit - **vista** Vista 3D Recognized file extensions: .-, .V, .VISTA, .v, .vista Supported element types: 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 - **vti** 3D image VTK-XML in- and output (experimental). Recognized file extensions: .VTI, .vti Supported element types: 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 - **vtk** 3D VTK image legacy in- and output (experimental). Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage Supported element types: 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 ## PLUGINS: 3dimage/maskedcost - **lncc** local normalized cross correlation with masking support., supported parameters are: *w* = 5; uint in \[1, 256\] half width of the window used for evaluating the localized cross correlation. - **mi** Spline parzen based mutual information with masking., supported parameters are: *cut* = 0; float in \[0, 40\] Percentage of pixels to cut at high and low intensities to remove outliers. *mbins* = 64; uint in \[1, 256\] Number of histogram bins used for the moving image. *mkernel* = \[bspline:d=3\]; factory Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel *rbins* = 64; uint in \[1, 256\] Number of histogram bins used for the reference image. *rkernel* = \[bspline:d=0\]; factory Spline kernel for reference image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel - **ncc** normalized cross correlation with masking support. (no parameters) - **ssd** Sum of squared differences with masking. (no parameters) ## PLUGINS: 3dimage/shape - **18n** 18n neighborhood 3D shape creator (no parameters) - **26n** 26n neighborhood 3D shape creator (no parameters) - **6n** 6n neighborhood 3D shape creator (no parameters) - **sphere** Closed spherical shape neighborhood including the pixels within a given radius r., supported parameters are: *r* = 2; float in (0, inf) sphere radius. ## PLUGINS: 3dtransform/io - **bbs** Binary (non-portable) serialized IO of 3D transformations Recognized file extensions: .bbs - **datapool** Virtual IO to and from the internal data pool Recognized file extensions: .@ - **vista** Vista storage of 3D transformations Recognized file extensions: .v, .v3dt - **xml** XML serialized IO of 3D transformations Recognized file extensions: .x3dt ## EXAMPLE mia-3dcost ## AUTHOR(s) Gert Wollny ## COPYRIGHT This software is Copyright (c) 1999‐2015 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'.