imagedata-registration
Advanced tools
################################# Image registration with imagedata #################################
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Helper modules to do
image registration for Imagedata Series objects.
Available modules #################
NPreg by Erlend Hodneland is implemented in Python,
and available as a self-supported PyPi package.
There are three implementations of NPreg:
CuPy and CUDA Toolkit.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.
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 itk-elastix
(https://github.com/InsightSoftwareConsortium/ITKElastix)
Python library is one particular interface to the Elastix/ITK routines.
Prerequisites #############
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
The imagedata-registration FSL module is a wrapper around the official FSL tools. A native FSL installation is required on the host computer.
ITK-Elastix is installed automatically as a dependency for this package.
Installation ############
.. code-block::
pip install imagedata-registration
Examples ########
NPreg examples <docs/NPreg.rst>_
FSL examples <docs/FSL.rst>_
ITK-Elastix examples <docs/ITKElastix.rst>_
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FAQs
Image registration routines for Imagedata
We found that imagedata-registration demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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