Projects

MNE

MEG and EEG data analysis in Python

Iod

Iod (Implementation Of Dynamic-Causal -Modelling) provides functionality to analyze (intracranial) EEG/MEG and fMRI data in terms of connectivity of predetermined brain regions utilizing the DCM method.

neuroimagingframework

NEWS (2010.03.16) - Neuroimaging Framework v0.8.1 is our new Featured Download! NEWS (2010.03.09) - Neuroimaging Framework v0.8.0 is our new Featured Download! NEWS (2010.03.08) - New development branch cut, Checkout Now! This is a work in progress. To contribute, contanct me: ... [More] "timothy.okeefe" at domain "gmail.com" What Neuroimaging Framework is Neuroimaging Framework (NIF) is an open source, software development toolkit (and framework) for Neuroimaging research. NIF was designed so that a majority of the core framework classes are independently useful e.g. \Neuro\Data\Nifti, \Neuro\Data\Dicom while others are designed to pull components together into a full pipeline execution framework. What Neuroimaging Framework isn't Neuroimaging Framework (NIF) is not another toolkit with it's own native implementations of algorithms, formats, etc. rather NIF aims to provide a consistent API to a growing number of software packages including: DCMTK, XNAT, AFNI, SPM, FSL, Freesurfer, etc. Through Neuroimaging Framework, one can generate simple to complex workflows without having to focus on the many details and idiosyncrasies that exist within and in between software packages. How easy is Neuroimaging Framework? Neuroimaging Framework is meant to be fall-over easy to use. As long as your script starts out like so: #!/usr/bin/php <? require_once getenv('NIF') . '/Neuro.php';You are ready to roll! Want a better example? Say you want to average several NIFTI files. With Neuroimaging Framework this could be accomplished with just a few lines of code: #!/usr/bin/php <? require_once getenv('NIF') . '/Neuro.php'; use Neuro\Data\NiftiCollection as NiftiCollection; use Neuro\Common\Logger as Logger; $logger = Logger::getInstance(); try { $collection = new NiftiCollection(); $collection->add("/path/to/s001.nii.gz"); $collection->add("/path/to/s002.nii.gz"); $nifti = $collection->mean(); $nifti->saveTo("./", "averaged"); } catch(\Exception $e) { $logger->fatal($e); }One of our fundamental goals is code clarity, from our choice of programming language all the way down to the most minuscule of design decisions. If you're scratching your head wondering what the above code does, we have failed to deliver. System Requirements If you're unsure your system is equipped for using Neuroimaging Framework, we've included a configure script to help you. After you've downloaded NIF, simply run: user@localhost: ./configurefrom within the bin directory and you'll know how capable is your system. If it is flat-out incapable, fire off an email. Dear Developers For those who have downloaded and installed the latest PHP Development Tools Project IDE, contributing to the project couldn't be easier. We've included our Eclipse project file within the project itself. So just checkout the latest source and even you could help us break things! Looking for a similar framework written in Python? Check out NIPYPE [Less]

ptsa

ptsa (pronounced pizza) is a Python module for performing time series analysis. Although it is specifically designed with neural data in mind (EEG, MEG, fMRI, etc...), the code should be applicable to almost any type of time series. At the foundation of ptsa is a subclass of the NumPy ndarray ... [More] called DimArray, that allows for tracking dimension information as part of a ndarray. [Less]

rotmantools

Currently used for ERP and MEG labs only

loreta

Methods and algorithms for pattern recognition and signal processing of the electroencephalogram (EEG), with emphasis on the analysis of computed electric neuronal activity.

nutmeg

An open source Matlab toolbox for processing MEG data.