This is old now. Use nilearn's plotting library for this!!
from nilearn import plotting
plotting.view_stat_map("/path/to/file")Want to see 3D brain data in the IPython_ notebook? Now you can by using Papaya_, a Javascript library for viewing medical images in the browser, and this little bit of code.
Clone this repository to your computer,
git clone https://github.com/akeshavan/nbpapaya
then add submodules
git submodule update --init --recursive
and run the setup script.
python setup.py install
Open a new IPython_ notebook
from nbpapaya import Brain, clear_brain
Then show a brain:
Brain("/path/to/your/brain.nii",port=<your ipython notebook port. Default is 8888>)
Or show overlaid brains
Brain(["/path/to/brain1.nii","/path/to/brain2.nii"],8888)
You can play around with the color maps and intensity ranges on the Papaya_ javascript interface.
Also, some files are created in the directory of your notebook to make it work. When you're done, clean up:
clear_brain()
The file papaya_viewer.html and the papaya_data folder are deleted.
Things might go wrong because I wrote this quickly. If you don't see anything, make sure you called Brain with the correct port. If you did, make sure that papaya.js and papaya.css exist in ~/.ipython/profile_default/static/custom/. If nothing is there, move the files in there. Also email me: akeshavan@ucla.edu.
.. _IPython: http://ipython.org/notebook.html .. _Papaya: https://github.com/rii-mango/Papaya/