--- name: "mia-2dmany2one-nonrigid" 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-2dmany2one-nonrigid" --- # mia-2dmany2one-nonrigid(1) Registration of a series of 2D images ## NAME mia-2dmany2one-nonrigid - Registration of a series of 2D images ## SYNOPSIS **mia-2dmany2one-nonrigid -i \ -o \ \[options\] \** ## DESCRIPTION **mia-2dmany2one-nonrigid** This program registers all images of a conscutively numbered set of images to one common user defined reference. ## OPTIONS ### File-IO - \-i --in-file=(input, required); string input perfusion data set - \-o --out-file=(output, required); string file name for registered images, numbering and pattern are deducted from the input data ### Registration - \-O --optimizer=gsl:opt=gd,step=0.1 Optimizer used for minimization - \-l --mg-levels=3 multi-resolution levels - \-f --transForm=spline transformation type\ For supported plugins see PLUGINS:2dimage/transform - \-r --ref=-1 reference frame (-1 == use image in the middle) - \-k --skip=0 skip registration of these images at the beginning of the series ### 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/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: 2dimage/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. - **lsd** Least-Squares Distance measure (no parameters) - **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. Various evaluation kernels are available., supported parameters are: *eval* = ds; dict plugin subtype. Supported values are: *sq* ‐ square of difference *ds* ‐ square of scaled difference *dot* ‐ scalar product kernel *cross* ‐ cross product kernel - **ssd** 2D imaga 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** 2D 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: 2dimage/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:2dimage/cost *debug* = 0; bool Save intermediate resuts for debugging. *ref* =(input, io) Reference image. For supported file types see PLUGINS:2dimage/io *src* =(input, io) Study image. For supported file types see PLUGINS:2dimage/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: *debug* = 0; int in \[0, 1\] write the distance transforms to a 3D image. *maxlabel* = 256; int in \[2, 32000\] maximum number of labels to consider. *ref* =(input, io) Reference image. For supported file types see PLUGINS:2dimage/io *src* =(input, io) Study image. For supported file types see PLUGINS:2dimage/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 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:2dimage/maskedcost *ref* =(input, io) Reference image. For supported file types see PLUGINS:2dimage/io *ref-mask* =(input, io) Reference image mask (binary). For supported file types see PLUGINS:2dimage/io *src* =(input, io) Study image. For supported file types see PLUGINS:2dimage/io *src-mask* =(input, io) Study image mask (binary). For supported file types see PLUGINS:2dimage/io *weight* = 1; float weight of cost function. ## PLUGINS: 2dimage/io - **bmp** BMP 2D-image input/output support. The plug-in supports reading and writing of binary images and 8-bit gray scale images. read-only support is provided for 4-bit gray scale images. The color table is ignored and the pixel values are taken as literal gray scale values. Recognized file extensions: .BMP, .bmp Supported element types: binary data, unsigned 8 bit - **datapool** Virtual IO to and from the internal data pool Recognized file extensions: .@ - **dicom** 2D image io for DICOM Recognized file extensions: .DCM, .dcm Supported element types: signed 16 bit, unsigned 16 bit - **exr** a 2dimage io plugin for OpenEXR images Recognized file extensions: .EXR, .exr Supported element types: unsigned 32 bit, floating point 32 bit - **jpg** a 2dimage io plugin for jpeg gray scale images Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg Supported element types: unsigned 8 bit - **png** a 2dimage io plugin for png images Recognized file extensions: .PNG, .png Supported element types: binary data, unsigned 8 bit, unsigned 16 bit - **raw** RAW 2D-image output support Recognized file extensions: .RAW, .raw 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 - **tif** TIFF 2D-image input/output support Recognized file extensions: .TIF, .TIFF, .tif, .tiff Supported element types: binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit - **vista** a 2dimage io plugin for vista images 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 ## PLUGINS: 2dimage/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: 2dimage/transform - **affine** Affine transformation (six degrees of freedom)., supported parameters are: *imgboundary* = mirror; factory image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = \[bspline:d=3\]; factory image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel - **rigid** Rigid transformations (i.e. rotation and translation, three degrees of freedom)., supported parameters are: *imgboundary* = mirror; factory image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = \[bspline:d=3\]; factory image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel *rot-center* = \[\[0,0\]\]; 2dfvector Relative rotation center, i.e. \<0.5,0.5\> corresponds to the center of the support rectangle. - **rotation** Rotation transformations (i.e. rotation about a given center, one degree of freedom)., supported parameters are: *imgboundary* = mirror; factory image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = \[bspline:d=3\]; factory image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel *rot-center* = \[\[0,0\]\]; 2dfvector Relative rotation center, i.e. \<0.5,0.5\> corresponds to the center of the support rectangle. - **spline** Free-form transformation that can be described by a set of B-spline coefficients and an underlying B-spline kernel., supported parameters are: *anisorate* = \[\[0,0\]\]; 2dfvector anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value.. *imgboundary* = mirror; factory image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = \[bspline:d=3\]; factory image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel *kernel* = \[bspline:d=3\]; factory transformation spline kernel.. For supported plug-ins see PLUGINS:1d/splinekernel *penalty* = ; factory Transformation penalty term. For supported plug-ins see PLUGINS:2dtransform/splinepenalty *rate* = 10; float in \[1, inf) isotropic coefficient rate in pixels. - **translate** Translation only (two degrees of freedom), supported parameters are: *imgboundary* = mirror; factory image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = \[bspline:d=3\]; factory image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel - **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: *imgboundary* = mirror; factory image interpolation boundary conditions. For supported plug-ins see PLUGINS:1d/splinebc *imgkernel* = \[bspline:d=3\]; factory image interpolator kernel. For supported plug-ins see PLUGINS:1d/splinekernel ## PLUGINS: 2dtransform/splinepenalty - **divcurl** divcurl penalty on the transformation, supported parameters are: *curl* = 1; float in \[0, inf) penalty weight on curl. *div* = 1; float in \[0, inf) penalty weight on divergence. *norm* = 0; bool Set to 1 if the penalty should be normalized with respect to the image size. *weight* = 1; float in (0, inf) weight of penalty energy. ## EXAMPLE Register the image series given by images 'inputXXXX.png' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registeredXXXX.png'. mia-2dmany2one-nonrigid -i input0000.png -o registered%04d.png -k 2 -r 30 image:cost=mi divcurl:weight=5 ## 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'.