mia-3drigidreg(1)

📦
version 2.4.7 · 2 versions
, in ubuntu jammy, ubuntu resolute, ubuntu stonking

✨ mia-3drigidreg(1) ✨

okay so bestie — this is the General Commands Manual page for mia-3drigidreg, and it's giving linear registration of 3D images. 💖

🌸 NAME 🌸

mia-3drigidreg — Linear registration of 3D images. 💅

🦋 SYNOPSIS 🦋

mia-3drigidreg -i <in-image> -r <ref-image> -o <out-image> [options]

💅 DESCRIPTION 💅

So mia-3drigidreg is literally the program that implements the registration of two gray scale 3D images. The transformation is not penalized, so you should only use translation, rigid, or affine transformations as target. And if you need nonrigid registration? Run mia-3dnonrigidreg instead. periodt. ✨

👑 OPTIONS 👑

🍓 File I/O 🍓

  • -i, --in-image=(input, required) — test image 💖 For supported file types see PLUGINS:3dimage/io. (io)
  • -r, --ref-image=(input, required) — reference image 🌸 For supported file types see PLUGINS:3dimage/io. (io)
  • -o, --out-image=(output, required) — registered output image 🎀 For supported file types see PLUGINS:3dimage/io. (io)
  • -t, --transformation=(output) — transformation output file name 🦋 For supported file types see PLUGINS:3dtransform/io. (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). yes bestie, “Maxiumum” is spelled like that in the original 💀

💜 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 🌈

okay bestie, this is the fun one — the whole point of the program, honestly. These plugins are the actual transformations, the glow-ups your image is about to get. Every single one of them is a "transformation plug-in", and they all speak the same two-parameter dialect when it comes to interpolation. So let's meet the cast 💅

affine 👑

Affine transformation (12 degrees of freedom). Yeah, twelve. Full send. Supported parameters are:

  • imgboundary = mirror; factory — image interpolation boundary conditions. Curious which plug-ins you can slot in here? Go peep PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins live in PLUGINS:1d/splinekernel ✨

axisrot 🎀

Restricted rotation transformation (1 degrees of freedom). Not the whole shebang — the transformation is locked to 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. Supported plug-ins? PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: PLUGINS:1d/splinekernel ✨
  • origin =(required, 3dfvector) — center of the transformation.

raffine 🌸

Restricted affine transformation (3 degrees of freedom). It's giving "affine but on a budget" — the transformation is restricted to rotation around the given axis plus shearing along the two axes perpendicular to the given one. Supported parameters are:

  • axis =(required, 3dfvector) — rotation axis.
  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins over at PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins over at PLUGINS:1d/splinekernel ✨
  • origin =(required, 3dfvector) — center of the transformation.

rigid 💪

Rigid transformation, i.e. rotation and translation (six degrees of freedom). No stretching, no squishing, just vibes and movement. Supported parameters are:

  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins: PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: 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. So yes bestie, <0.5,0.5,0.5> = dead center, main character position 👑

rotation 🌀

Rotation transformation (three degrees of freedom). Just spin, no translate. Supported parameters are:

  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins: PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: 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. (Same deal as rigid, <0.5,0.5,0.5> = absolute center of the volume ✨)

rotbend 🌈

Restricted transformation (4 degrees of freedom). The transformation is restricted to 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. (yes, that typo is canon, we keep it, character-for-character, no cap 💀). Supported parameters are:

  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins: PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: 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. This is the "make it whatever you want" one, the unlimited creative mode. Supported parameters are:

  • anisorate = [[0,0,0]]; 3dfvector — anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the rate value.. (double period, iconic, we stan punctuation)
  • debug = 0; bool — enable additional debugging output.
  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins: PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: 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). Pure sliding, no rotation, we simply move. Supported parameters are:

  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins: PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: 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. So like, a whole custom translation field, point by point, per grid point. Supported parameters are:

  • imgboundary = mirror; factory — image interpolation boundary conditions. Supported plug-ins: PLUGINS:1d/splinebc 🦋
  • imgkernel = [bspline:d=3]; factory — image interpolator kernel. Supported plug-ins: PLUGINS:1d/splinekernel ✨

💾 PLUGINS: 3dtransform/io 💾

Now that we can transform stuff, we gotta be able to save it and load it back, right? These are the IO girlies for 3D transformations. Each one lists the file extensions it recognizes — and bestie, the extension is literally how the program figures out which plug-in you want, so type them exactly 💅

bbs 📦

Binary (non-portable) serialized IO of 3D transformations

  • Recognized file extensions: .bbs
⚠️ Heads up: this one is non-portable. It does the job, but don't be surprised if it doesn't travel well between setups, fr fr.

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 🧮

Ooh, penalty terms. These tell the optimizer "hey, don't do that, it's ugly" — mathematically. Great for keeping your transformation smooth and well-behaved instead of chaotic and unhinged 😌✨

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.

gdas</p> — gradient descent, but make it self-correcting ✨

Bestie, this one is gradient descent with automatic step size correction. Here's the vibe-check on its parameters:

  • ftolr = 0; double in [0, inf) — Stop if the relative change of the criterion is below this.
  • 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</p> — gradient descent with quadratic step estimation 🦋

It estimates the step size quadratically. Fancy. Its parameters:

  • ftolr = 0; double in [0, inf) — Stop if the relative change of the criterion is below this.
  • 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</p> — the GNU Scientific Library minimizers 💜

This optimizer plugin is built on the multimin optimizers of the GNU Scientific Library (GSL), https://www.gnu.org/software/gsl/. Parameters go like:

  • 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</p> — minimizer algorithms via the NLOPT library 🌈

Minimizer algorithms using the NLOPT library. For a description of the optimizers, please see 'http://ab-initio.mit.edu/wiki/index.php/NLopt_Algorithms'. Its parameters:

  • 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 🌸

Okay so picture this: register image test.v to image ref.v affine, and write the registered image out to reg.v. Use two multiresolution levels and ssd as the cost function. Iconic behavior, honestly:

mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd

💅 AUTHOR(s) 💅

Gert Wollny 👑

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'.

And that's the whole page, bestie — every last flag, algorithm and boundary preserved, no cap. 🫶 This one's from the USER COMMANDS corner of the manual, version v2.4.7, filed under mia-3drigidreg(1). Go register something cute. 💖✨

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