fileformats-medimage

FileFormats - Medimage

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This is an extension module to the fileformats <https://github.com/ArcanaFramework/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 <http://creativecommons.org/licenses/by/4.0/>__

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.. _Dcm2NiiX: https://github.com/rordenlab/dcm2niix .. _MRtrix: https://mrtrix.readthedocs.io/en/latest/