Coregistration options#
This section provides information about the arguments that can be
passed to mdreg.fit to control the coregistration process. These arguments
are provided as a dictionary referred to as fit_coreg in the mdreg.fit
function.
By default, mdreg uses the elastix package for coregistration, with default
parameters. The options allow the user to control the coregistration package
used, and the optional parameters which can be controlled within the
different packages.
Elastix#
Elastix is one of the coregistration engines available to perform
the coregistration components in mdreg. For consistent usage
across different coregistration engines, mdreg contains pythonic wrappers
for the core functionality available in elastix, but the functionality is
not otherwise modified.
We refer to the original elastix pages for more detail on elastix. Please note elastix authors request that the following papers are cited if you use the elastix software anywhere:
S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, “elastix: a toolbox for intensity based medical image registration, “ IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010.
D.P. Shamonin, E.E. Bron, B.P.F. Lelieveldt, M. Smits, S. Klein and M. Staring, “Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer’s Disease”, Frontiers in Neuroinformatics, vol. 7, no. 50, pp. 1-15, January 2014.
mdreg uses the interface itk-elastix which is based on SimpleElastix,
created by Kasper Marstal:
Kasper Marstal, Floris Berendsen, Marius Staring and Stefan Klein, “SimpleElastix: A user-friendly, multi-lingual library for medical image registration”, International Workshop on Biomedical Image Registration (WBIR), Las Vegas, Nevada, USA, 2016.