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qp Quantiphyse

screenshots/sample_image.png

Quantiphyse is a viewing and analysis tool for 3D and 4D biomedical data. It is particularly suited for physiological or functional imaging data comprised of multi volumes in a 4D (time-) series and/or multimodal imaging data. Quantiphyse is built around the concept of making spatially resolved measurements of physical or physiological processes from imaging data using either model-based or model-free methods, in a large part exploiting Bayesian inference techniques. Quantiphyse can analyse data both voxelwise or within regions of interest that may be manually or automatically created, e.g. supervoxel or clustering methods.

screenshots/collage.png

Features

  • 2D orthographic viewing and navigation of data, regions of interest (ROIs) and overlays
  • Universal analysis tools including clustering, supervoxel generation and curve comparison
  • Tools for CEST, ASL, DCE and DSC-MRI analysis and modelling
  • Integration with selected FSL tools
  • ROI generation
  • Registration and motion correction
  • Extensible via plugins

License

© 2017-2019 University of Oxford

Quantiphyse is free for non commercial use. The license details are displayed on first use and the LICENSE file is included in the distribution. For further information contact the OUI Software Store. If you are interested in commercial licensing you shold contact OUI in the first instance.

Tutorials

Download

Quantiphyse is available on PyPi - see :ref:`install`.

Major releases of Quantiphyse are also available via the Oxford University Innovation Software Store. The packages held by OUI have no external dependencies and can be installed on Windows, Mac and Linux. They may lag behind the current PyPi release in terms of functionality.

Plugins

Some of the functionality described in this documentation requires the installation of plugins. The following plugins are available:

  • quantiphyse-dce - DCE modelling
  • quantiphyse-fabber - Bayesian model fitting - required for various specialised tools
  • quantiphyse-fsl - Interface to selected FSL tools (requires FSL installation)
  • quantiphyse-cest - CEST-MRI modelling (requires quantiphyse-fabber)
  • quantiphyse-asl - ASL-MRI modelling (requires FSL installation and quantiphyse-fabber)
  • quantiphyse-dsc - DSC-MRI modellingg (requires quantiphyse-fabber)
  • quantiphyse-t1 - T1 mapping (requires quantiphyse-fabber)

Plugins are installed from PyPi, e.g.:

pip install quantiphyse-dce

They will be automatically detected and added to Quantiphyse next time you run it. The packages available on the OUI software store have all plugins included which were available at the time of release.

User Guide

Basic functions

.. toctree::
   :maxdepth: 2

   overview
   getting_started
   overlay_stats
   modelfit

Generic analysis and processing tools

.. toctree::
   :maxdepth: 1

   compare
   curve_compare
   simple_maths
   reg
   smoothing
   cluster
   sv
   roi_analysis
   roibuilder
   mean_values
   hist
   rp

Tools from plugins

.. toctree::
   :maxdepth: 1

   t1
   pk
   cest
   asl_overview

Advanced Tools

.. toctree::
   :maxdepth: 1

   batch
   console
   nifti_extension
   faq

Bugs/Issues

Please report bug, issues, feature requests or other comments to the current maintainer:

Contributors

Acknowledgements

  • Julia Schnabel
  • Sir Mike Brady

Images copyright 2018 University of Oxford