Description:
imagedataregistration 0.2.4
Helper modules to do
image registration for Imagedata Series objects.
Available modules
NPreg
NPreg by Erlend Hodneland is implemented in Python,
and available as a self-supported PyPi package.
There are three implementations of NPreg:
Pure Python/NumPy code. Source code will run on any Python platform.
Cython code. Binary code compiled for supported platforms.
CuPy/CUDA code. Source code which will run on platforms with a working CuPy and CUDA Toolkit.
FSL
FSL
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)
has several methods for image registration.
Using FSL image registration from Python requires the FSL interface from
nipype, as well as a the FSL executables.
Each FSL method may have different requirements.
The common factor is that FSL methods will read and write NIfTI image files.
A function register_fsl is provided here.
This function will register a moving Series to a fixed Series.
The default registration method is fsl.MCFLIRT.
The function will accept other registration methods.
ITK Elastix
The popular Elastix GUI is based on the C++ ITK image registration routines.
Like the FSL methods, there are numerous Elastix methods available, all with
different requirements.
The SimpleElastix
(https://simpleelastix.readthedocs.io/index.html)
Python library is one particular interface to the Elastix/ITK routines.
Prerequisites
NPreg on CUDA GPU
imagedata-registration will benefit from a CUDA GPU. If this is available,
install CuPy (https://docs.cupy.dev).
First, install the CUDA Toolkit: see https://developer.nvidia.com/cuda-toolkit.
There are different options for installing CuPy. See:
https://docs.cupy.dev/en/stable/install.html
FSL
The imagedata-registration FSL module is a wrapper around the official FSL tools.
A native FSL installation is required on the host computer.
SimpleElastix
SimpleElastix must be installed separately:
pip install SimpleITK-SimpleElastix
Installation
pip install imagedata-registration
Examples
NPreg examples
FSL examples
SimpleElastix examples
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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