Installation of Quantiphyse

This page describes the recommended installation method for Quantiphyse.

There are a number of other ways you can install the application - see Other options for Quantiphyse installation, however unless you have a good working knowledge of Python and virtual environments we recommend you use this method which has been tested on a number of platforms.

If you find a problem with these instructions, please report it using the Issue Tracker.

Note

To use some plugins you’ll need to have a working FSL installation. For more information go to FSL installation.

Installing Anaconda

Anaconda (https://www.anaconda.org) is an easy to install distribution of Python which importantly includes the conda tool for installing packages in isolated environments.

You will need to install the Anaconda environment before using any of these recipes. When selecting a Python version, chose version 3.

Once Anaconda is installed and the conda tool is working, follow the instructions below:

Note

If you have FSL installed, you already have conda installed in $FSLDIR/fslpython/bin/ You can still install Anaconda separately but alternatively you can add this directory to your PATH and use the conda there.

Installing Quantiphyse in a Conda environment

Note

In the future we hope to put Quantiphyse into conda itself so the whole process can consist of conda install quantiphyse.

We recommend Python 3.7 as a reasonably up to date version of Python for which dependencies are generally widely available. While Quantiphyse should be compatible with newer Python releases sometimes it is difficult to get matching versions of important dependencies such as Numpy.

To create a Python 3.7 environment and install Quantiphyse use the following commands:

conda create -n qp python=3.7
conda activate qp
pip install quantiphyse

On Mac you will also need to do:

pip install pyobjc

This installs the basic Quantiphyse app - you should be able to run it by typing ‘quantiphyse’ at the command line.

Note

For recent versions of Mac OS (e.g. Big Sur, Monterey) it is necessary to set the following environment variable before running Quantiphyse: export QT_MAC_WANTS_LAYER=1.

Note

PySide2 is not currently available for M1-based Macs. It is possible to install Quantiphyse by using the Rosetta terminal to emulate an i386 environment. You will need to install Miniconda/Anaconda within Rosetta and then use that version of Conda to create an environment for Quantiphyse and then follow the instructions above.

Installing plugins

To install plugins use pip, for example this is to install all current pure-python plugins:

pip install quantiphyse-cest quantiphyse-asl quantiphyse-qbold quantiphyse-dsc quantiphyse-fsl quantiphyse-sv quantiphyse-datasim

Installing plugins requiring compilation

A few plugins contain C/C++ code and not just Python. Currently these plugins are:

quantiphyse-t1 quantiphyse-dce quantiphyse-deeds

To install these you may need to ensure you have a working build environment, as follows:

Mac

Install command line tools from: https://anansewaa.com/install-command-line-tools-on-macos-catalina/

Once the build environment is installed you can pip install the plugins as normal.