--- name: "mia-3drigidreg" 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-3drigidreg" --- # mia-3drigidreg(1) Linear registration of 3D images. ## NAME mia-3drigidreg - Linear registration of 3D images. ## SYNOPSIS **mia-3drigidreg -i \ -r \ -o \ \[options\]** ## DESCRIPTION **mia-3drigidreg** This program implements the registration of two gray scale 3D images. The transformation is not penalized, therefore, one should only use translation, rigid, or affine transformations as target and run mia-3dnonrigidreg of nonrigid registration is to be achieved. ## OPTIONS ### File I/O - \-i --in-image=(required, input); io test image\ For supported file types see PLUGINS:3dimage/io - \-r --ref-image=(required, input); io reference image\ For supported file types see PLUGINS:3dimage/io - \-o --out-image=(required, output); io registered output image\ For supported file types see PLUGINS:3dimage/io - \-t --transformation=(output); io transformation output file name\ For supported file types see PLUGINS:3dtransform/io - \-c --cost=ssd cost function\ For supported plugins see PLUGINS:3dimage/cost - \-l --levels=3 multigrid levels - \-O --optimizer=gsl:opt=simplex,step=1.0 Optimizer used for minimization\ For supported plugins see PLUGINS:minimizer/singlecost - \-f --transForm=rigid transformation type\ For supported plugins see PLUGINS:3dimage/transform ### 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: 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/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/transform - **affine** Affine transformation (12 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 - **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: *axis* =(required, 3dfvector) rotation axis. *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 *origin* =(required, 3dfvector) center of the transformation. - **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: *axis* =(required, 3dfvector) rotation axis. *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 *origin* =(required, 3dfvector) center of the transformation. - **rigid** Rigid transformation, i.e. rotation and translation (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 *origin* = \[\[0,0,0\]\]; 3dfvector Relative rotation center, i.e. \<0.5,0.5,0.5\> corresponds to the center of the volume. - **rotation** Rotation transformation (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 *origin* = \[\[0,0,0\]\]; 3dfvector Relative rotation center, i.e. \<0.5,0.5,0.5\> corresponds to the center of the volume. - **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: *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 *norot* = 0; bool Don't optimize the rotation. *origin* =(required, 3dfvector) center of the transformation. - **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* = \[\[0,0,0\]\]; 3dfvector anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value.. *debug* = 0; bool enable additional debugging output. *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 energy term. For supported plug-ins see PLUGINS:3dtransform/splinepenalty *rate* = 10; float in \[1, inf) isotropic coefficient rate in pixels. - **translate** 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 - **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: 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 ## PLUGINS: 3dtransform/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. ## PLUGINS: minimizer/singlecost - **gdas** Gradient descent with automatic step size correction., supported parameters are: *ftolr* = 0; double in \[0, inf) Stop if the relative change of the criterion is below.. *max-step* = 2; double in (0, inf) Maximal absolute step size. *maxiter* = 200; uint in \[1, inf) Stopping criterion: the maximum number of iterations. *min-step* = 0.1; double in (0, inf) Minimal absolute step size. *xtola* = 0.01; double in \[0, inf) Stop if the inf-norm of the change applied to x is below this value.. - **gdsq** Gradient descent with quadratic step estimation, supported parameters are: *ftolr* = 0; double in \[0, inf) Stop if the relative change of the criterion is below.. *gtola* = 0; double in \[0, inf) Stop if the inf-norm of the gradient is below this value.. *maxiter* = 100; uint in \[1, inf) Stopping criterion: the maximum number of iterations. *scale* = 2; double in (1, inf) Fallback fixed step size scaling. *step* = 0.1; double in (0, inf) Initial step size. *xtola* = 0; double in \[0, inf) Stop if the inf-norm of x-update is below this value.. - **gsl** optimizer plugin based on the multimin optimizers of the GNU Scientific Library (GSL) https://www.gnu.org/software/gsl/, supported parameters are: *eps* = 0.01; double in (0, inf) gradient based optimizers: stop when \|grad\| \< eps, simplex: stop when simplex size \< eps.. *iter* = 100; uint in \[1, inf) maximum number of iterations. *opt* = gd; dict Specific optimizer to be used.. Supported values are: *simplex* ‐ Simplex algorithm of Nelder and Mead *cg-fr* ‐ Flecher-Reeves conjugate gradient algorithm *cg-pr* ‐ Polak-Ribiere conjugate gradient algorithm *bfgs* ‐ Broyden-Fletcher-Goldfarb-Shann *bfgs2* ‐ Broyden-Fletcher-Goldfarb-Shann (most efficient version) *gd* ‐ Gradient descent. *step* = 0.001; double in (0, inf) initial step size. *tol* = 0.1; double in (0, inf) some tolerance parameter. - **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: *ftola* = 0; double in \[0, inf) Stopping criterion: the absolute change of the objective value is below this value. *ftolr* = 0; double in \[0, inf) Stopping criterion: the relative change of the objective value is below this value. *higher* = inf; double Higher boundary (equal for all parameters). *local-opt* = none; dict local minimization algorithm that may be required for the main minimization algorithm.. Supported values are: *gn-direct* ‐ Dividing Rectangles *gn-direct-l* ‐ Dividing Rectangles (locally biased) *gn-direct-l-rand* ‐ Dividing Rectangles (locally biased, randomized) *gn-direct-noscal* ‐ Dividing Rectangles (unscaled) *gn-direct-l-noscal* ‐ Dividing Rectangles (unscaled, locally biased) *gn-direct-l-rand-noscale* ‐ Dividing Rectangles (unscaled, locally biased, randomized) *gn-orig-direct* ‐ Dividing Rectangles (original implementation) *gn-orig-direct-l* ‐ Dividing Rectangles (original implementation, locally biased) *ld-lbfgs-nocedal* ‐ None *ld-lbfgs* ‐ Low-storage BFGS *ln-praxis* ‐ Gradient-free Local Optimization via the Principal-Axis Method *ld-var1* ‐ Shifted Limited-Memory Variable-Metric, Rank 1 *ld-var2* ‐ Shifted Limited-Memory Variable-Metric, Rank 2 *ld-tnewton* ‐ Truncated Newton *ld-tnewton-restart* ‐ Truncated Newton with steepest-descent restarting *ld-tnewton-precond* ‐ Preconditioned Truncated Newton *ld-tnewton-precond-restart* ‐ Preconditioned Truncated Newton with steepest-descent restarting *gn-crs2-lm* ‐ Controlled Random Search with Local Mutation *ld-mma* ‐ Method of Moving Asymptotes *ln-cobyla* ‐ Constrained Optimization BY Linear Approximation *ln-newuoa* ‐ Derivative-free Unconstrained Optimization by Iteratively Constructed Quadratic Approximation *ln-newuoa-bound* ‐ Derivative-free Bound-constrained Optimization by Iteratively Constructed Quadratic Approximation *ln-neldermead* ‐ Nelder-Mead simplex algorithm *ln-sbplx* ‐ Subplex variant of Nelder-Mead *ln-bobyqa* ‐ Derivative-free Bound-constrained Optimization *gn-isres* ‐ Improved Stochastic Ranking Evolution Strategy *none* ‐ don't specify algorithm *lower* = -inf; double Lower boundary (equal for all parameters). *maxiter* = 100; int in \[1, inf) Stopping criterion: the maximum number of iterations. *opt* = ld-lbfgs; dict main minimization algorithm. Supported values are: *gn-direct* ‐ Dividing Rectangles *gn-direct-l* ‐ Dividing Rectangles (locally biased) *gn-direct-l-rand* ‐ Dividing Rectangles (locally biased, randomized) *gn-direct-noscal* ‐ Dividing Rectangles (unscaled) *gn-direct-l-noscal* ‐ Dividing Rectangles (unscaled, locally biased) *gn-direct-l-rand-noscale* ‐ Dividing Rectangles (unscaled, locally biased, randomized) *gn-orig-direct* ‐ Dividing Rectangles (original implementation) *gn-orig-direct-l* ‐ Dividing Rectangles (original implementation, locally biased) *ld-lbfgs-nocedal* ‐ None *ld-lbfgs* ‐ Low-storage BFGS *ln-praxis* ‐ Gradient-free Local Optimization via the Principal-Axis Method *ld-var1* ‐ Shifted Limited-Memory Variable-Metric, Rank 1 *ld-var2* ‐ Shifted Limited-Memory Variable-Metric, Rank 2 *ld-tnewton* ‐ Truncated Newton *ld-tnewton-restart* ‐ Truncated Newton with steepest-descent restarting *ld-tnewton-precond* ‐ Preconditioned Truncated Newton *ld-tnewton-precond-restart* ‐ Preconditioned Truncated Newton with steepest-descent restarting *gn-crs2-lm* ‐ Controlled Random Search with Local Mutation *ld-mma* ‐ Method of Moving Asymptotes *ln-cobyla* ‐ Constrained Optimization BY Linear Approximation *ln-newuoa* ‐ Derivative-free Unconstrained Optimization by Iteratively Constructed Quadratic Approximation *ln-newuoa-bound* ‐ Derivative-free Bound-constrained Optimization by Iteratively Constructed Quadratic Approximation *ln-neldermead* ‐ Nelder-Mead simplex algorithm *ln-sbplx* ‐ Subplex variant of Nelder-Mead *ln-bobyqa* ‐ Derivative-free Bound-constrained Optimization *gn-isres* ‐ Improved Stochastic Ranking Evolution Strategy *auglag* ‐ Augmented Lagrangian algorithm *auglag-eq* ‐ Augmented Lagrangian algorithm with equality constraints only *g-mlsl* ‐ Multi-Level Single-Linkage (require local optimization and bounds) *g-mlsl-lds* ‐ Multi-Level Single-Linkage (low-discrepancy-sequence, require local gradient based optimization and bounds) *ld-slsqp* ‐ Sequential Least-Squares Quadratic Programming *step* = 0; double in \[0, inf) Initial step size for gradient free methods. *stop* = -inf; double Stopping criterion: function value falls below this value. *xtola* = 0; double in \[0, inf) Stopping criterion: the absolute change of all x-values is below this value. *xtolr* = 0; double in \[0, inf) Stopping criterion: the relative change of all x-values is below this value. ## EXAMPLE Register image test.v to image ref.v affine and write the registered image to reg.v. Use two multiresolution levels and ssd as cost function. mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd ## 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'.