2025 Python Packaging Survey is now live!  Take the survey now

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

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for tclose from gravatar.com tclose

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: Apache Software License (Creative Commons Attribution 4.0 International Public License By exercising the Licensed Rights (def...)
  • Author: Thomas G. Close
  • Maintainer: Thomas G. Close
  • Tags data , file formats
  • Requires: Python >=3.8
Classifiers
Report project as malware

Project description

https://github.com/ArcanaFramework/fileformats-medimage/actions/workflows/tests.yml/badge.svg https://codecov.io/gh/ArcanaFramework/fileformats-medimage/branch/main/graph/badge.svg?token=UIS0OGPST7 Supported Python versions Latest Version

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 load methods use the extended install option to install additional dependencies required for these methods:

$ pip3 install fileformats-medimage[extended]

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

Creative Commons Attribution 4.0 International License

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page