Setup

Installing Dependencies

All dependencies are listed in requirements.txt. It’s a good idea to install everything into a virtual environment, but feel free to be young and reckless :O. Alternatively, the Anaconda python distribution contains all the necessary packages, except for nibabel, which can be installed using pip install nibabel.

Installing Pycorr

cd to the directory with pycorr, then python setup.py install. Since the package is still somewhat of a moving target, you might want to symlink it by using python setup.py develop.

Using pycorr on Rondo

pycorr is already installed in a virtual environment in the Hasson lab fileshare. Activate it by editing your PATH in ~/.local:

setenv PATH=/jukebox/hasson/michael/venv/anaconda:$PATH

Then, you can load the python environment by entering source activate trw-interl in the console.

If you have a different shell, such as bash, enabled by default–then it may be better to edit ~/.bash_login. Replace setenv with export.