Installing MedPy as user


All installation instructions are for Debian derivates, such as Ubuntu, but they should be simmilar for other distributions.

The local install will place MedPy in your user site-packages directory and does not require root privileges. You can find our the location of your personal site-packages directory by calling:

python -c 'import site;print site.USER_SITE'

In some cases, the Python configuration does not find packages in the users site-packages directory, in which case you will have to add it to your PYTHONPATH variable. To make this permanent, add the extension to your bashrc, e.g. using:

echo "export PYTHONPATH=${PYTHONPATH}:$( python -c 'import site;print site.USER_SITE' )" >> ~/.bashrc

More importantly, the script shipped with MedPy won’t be in your PATH and hence can not be used directly. If your user site-packages directory is e.g. /home/<user>/.local/lib/python2.7/site-packages/, the scripts are most likely to be found under /home/<user>/.local/bin/. Add this directory to your PATH using:

echo "export PATH=${PATH}:/home/<user>/.local/bin/" >> ~/.bashrc

(Don’t forget to replace <user> with your own user name.)

Installing using PIP

Requires PIP to be installed on your machine.

To enable the graph-cut package, we also need the following, which required administrator rights. If you do not plan on using the graph-cut functionality of MedPy, you can skip this step.

sudo apt-get install libboost-python-dev build-essential

To install MedPy itself, simply call

pip install --user medpy

Installing from source

No PIP? Download the sources from, unpack them, enter the directory and run

python install --user