Classes for representing various medical imaging file formats in Python classes for use in type hinting in data workflows
Project description
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 converter to work, you will also need to use the [extended] install option and 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
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