Basic reading support for AFNI in Python

This is a quick-and-dirty module to read AFNI BRIK/HEAD files in Python. I did very little testing, so please use with caution and if you find bugs, send me your suggested changes in exchange for my eternal gratitude!

Dedicated to the fine folks who built AFNI and made it available for everyone!

Usage (assumes that you have TT_N27+tlrc AFNI BRIK/HEAD files sitting in the directory where you run this from):

import afni
header,brik = afni.read('TT_N27+tlrc') # reads TT_N27+tlrc.{HEAD|BRIK}

That's it!

I also include an Jupyter notebook that shows how you can read AFNI data files and then work with it in Python. For that to work, you have to download example BRIK/HEAD files, for example from here.

Under Linux/Mac OS you can download these with wget (assuming that you have wget installed):

wget https://afni.nimh.nih.gov/pub/dist/src/TT_N27+tlrc.HEAD
wget https://afni.nimh.nih.gov/pub/dist/src/TT_N27+tlrc.BRIK.gz
gunzip TT_N27+tlrc.BRIK.gz

This has been tested with Python 3 but it should probably work under Python 2 as well.

Prerequisites

• numpy (to install it, run pip install numpy)

TODO

• Let Python read compressed (gzipped) .BRIK files.
• Test the that we scale values correctly (based on BRICK_FLOAT_FACS in the header).
• Integrate this into nibabel.