Medical Image Registration ToolKit (MIRTK)

The MIRTK is a research-focused image processing toolkit, developed at the BioMedIA research group. It provides a collection of libraries and command-line tools to assist in processing and analyzing imaging data. The main application of the MIRTK is in adult and neonatal brain MR image registration as well as the reconstruction of cortical surface meshes. The modular project organization of the MIRTK enables the installation of selected modules.

In the event you found the MIRTK useful, please consider giving appropriate credit to the software with a citation of the research article(s) describing the implemented algorithm(s). See the list of publications for suitable references.

Modules

Module	Brief Description
Common	Base classes and common functions. (required)
Numerics	Utility types such as matrices and functions for numerical optimization.
Image	Image containers, interpolators, and basic image processing filters.
I/O	I/O functions such as image and point set file readers and writers.
Point Set	VTK point set/surface filters. Required for point set/surface registration.
Transformation	Image and point set transformation types and regularization terms.
Registration	Image and point set registration library.
Deformable	Library for Euler integration of deformable meshes such as cortical surfaces.
Mapping	Filters for the mapping of brain surfaces and volumes.
Scripting	Collection of auxiliary modules for scripting languages such as Python.
Draw-EM	Structural and tissue segmentation of neonatal brain MR images.

Commands

aggregate-images	average-dofs	average-images	average-measure
average-overlap	bisect-dof	blend-surface	calculate-boundary-map
calculate-distance-map	calculate-element-wise	calculate-exponential-map	calculate-filtering
calculate-gradients	calculate-lie-bracket	calculate-logarithmic-map	calculate-surface-attributes
calculate-surface-map	calculate-surface-spectrum	calculate-volume-map	change-label
close-image	close-scalars	combine-images	compose-dofs
compose-maps	construct-atlas	convert-dof	convert-image
convert-pointset	copy-pointset-attributes	cut-brain	decimate-surface
deform-mesh	delete-pointset-attributes	detect-edges	dilate-image
dilate-scalars	downsample-image	draw-em	edit-dof
edit-image	em	em-hard-segmentation	erode-image
erode-scalars	evaluate-atlas	evaluate-cardiac-motion	evaluate-distance
evaluate-distortion	evaluate-dof	evaluate-jacobian	evaluate-overlap
evaluate-similarity	evaluate-surface-map	evaluate-surface-mesh	evaluate-surface-overlap
evaluate-volume-map	extract-connected-components	extract-connected-points	extract-image-region
extract-image-slice	extract-image-volume	extract-pointset-cells	extract-pointset-surface
extract-surface	fill-holes	fill-holes-nn-based	flip-image
help-rst	info	init-dof	invert-dof
kmeans	match-histogram	match-points	measure-volume
merge-surfaces	normalize	offset-surface	open-image
open-scalars	project-onto-surface	recon-neonatal-cortex	reflect-image
register	remesh-surface	resample-image	smooth-image
smooth-surface	split-labels	subdivide-brain-image	transform-image
transform-points

Background

Parts of the Common, Numerics, Image, Transformation, and Registration modules and command-line tools of the MIRTK originated from the IRTK written by Daniel Rueckert and Julia Schnabel. All of the transformation and registration code of the IRTK was rewritten from scratch by Andreas Schuh during his PhD studies, with a new modular and extended registration framework. Additional modules and commands for the reconstruction and inflation of cortical surface meshes, the registration of surface meshes, and the harmonic mapping of brain volumes were subsequently added to the MIRTK.