Processing tools for high-resolution neuroimaging
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
cbstools
doc
docker
examples
nighres
travis
.gitignore
.travis.yml
Dockerfile
LICENSE
MANIFEST.in
README.rst
build.sh
build_local_cbstools.sh
cbstools-lib-files.sh
setup.cfg
setup.py

README.rst

Travis CI build status Documentation Status

Nighres

Nighres is a Python package for processing of high-resolution neuroimaging data. It developed out of CBS High-Res Brain Processing Tools and aims to make those tools easier to install, use and extend.

Because parts of the package have to be built locally it is currently not possible to use pip install directly from PyPI. Instead, please follow the installation instructions provided at http://nighres.readthedocs.io/en/latest/installation.html

Currently, Nighres is developed and tested on Linux Ubuntu Trusty and Python 2.7. We hope to support all common Unix platforms and Python 3 soon.

Docker

To quickly try out nighres in a preset, batteries-included environment, you can use the included Dockerfile, which includes Ubuntu 14 Trusty, openJDK-8, nighres, and Jupyter Notebook. The only thing you need to install is Docker, a lightweight container platform that runs on Linux, Windows and Mac OS X.

To build the Docker image, do the following:

git clone https://github.com/nighres/nighres
cd nighres
docker build . -t nighres

To run the Docker container:

docker run --rm -p 8888:8888 nighres

Now go with your browser to https://localhost:8888 to start a notebook. You should be able to import nighres by entering:

import nighres

into the first cell of your notebook.

Usually you also want to have access to some data when you run nighres. You can grant the Docker container access to a data folder on your host OS by using the -v tag when you start the container:

docker run --rm -v /home/me/my_data:/data -p 8888:8888 nighres

Now, in your notebook you will be able to access your data on the path /data