NEWS (2010.09.29) - We are no longer maintaining a single repository for the PHP and Python codebases. A new Google Code Project has been created for the Neuroinfo Toolkit for Python developers.

To checkout, please checkout the latest code:

svn co http://neuroimagingframework.googlecode.com/svn/python/trunk Neuroinfo_Toolkit

This is a work in progress. To contribute, contanct me: "timothy.okeefe" at domain "gmail.com"

Neuroinfo Toolkit (NIT) is not another toolkit with native implementations of image processing algorithms... yet. We leverage a carefully chosen selection of Python modules and toolkits (e.g. PyNifti, FSL) in an attempt to provide a consistent and easy-to-use API for rapid analysis prototyping, data exploration, and interaction with data repositories.

We hope to alleviate several pain points in software development, especially those present in the Neuroimaging domain without adding unnecessary bloat.

Let's see some example code:

#!/usr/bin/env python

import neuro.app
from neuro.filesystem import *
from neuro.common import Logger
from neuro.nifti import Nifti

## --- setup logger
logger = Logger()
logger.info("Welcome to your first script")

## --- some variables and a log statement
file = "/data/file.nii.gz"
logger.info("Reading file: " + file)

## --- no more try catching all over the place thanks to neuro.app
nifti = Nifti(file)

## --- show some attributes
logger.info(nifti.getX())
logger.info(nifti.getY())
logger.info(nifti.getZ())
logger.info(nifti.getNumVolumes())
logger.info(nifti.getOrientation())

## --- flip orientation
nifti.swapOrientation()
logger.info("New orientation: " + nifti.getOrientation())
        
## --- fetch timeseries for a particular voxel
ts = nifti.getTimeseries(1, 1, 1)

## --- write out the timeseries to a file
filePutContents(ts, "~/timeseries.txt")

Not only is this code easy to read, it is actually more difficult to shoot yourself in the foot! This way, you can focus on making discoveries and spend less time on the tediums of software development.

And that is only the beginning.