fileformats-medimage 0.11.2

Classes for representing various medical imaging file formats in Python classes for use in type hinting in data workflows

This is an extension module to the fileformats package, which that adds support for commonly used medical imaging formats, such as DICOM (sets/directories), NIfTI, and MRtrix Image Format, etc…

Quick Installation

This extension can be installed for Python 3 using pip:

$ pip3 install fileformats-medimage

This will install the core package and any other dependencies to validate the file formats.

To use converters and metadata reading methods that depend on third-party packages, also install the associated extras package:

$ pip3 install fileformats-medimage-extras

For most of the converters to work, you will need to install the Dcm2NiiX and MRtrix software packages. There are various ways to do this, but on Ubuntu you can install Dcm2NiiX with:

$ sudo apt install libopenjp2-7
$ curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
$ unzip dcm2niix_lnx.zip
$ mv dcm2niix /usr/local/bin

(on Mac you can use Homebrew instead of apt to install libopenjp2-7). MRtrix can be installed with miniconda:

$ conda install -c mrtrix3 mrtrix3

License

This work is licensed under a Creative Commons Attribution 4.0 International License

Acknowledgements

The authors acknowledge the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy (NCRIS) capability.