NBT is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki with extensive help and tutorials.
Toolboxes for SPM (http://www.fil.ion.ucl.ac.uk/spm/) developed at Freiburg Brain Imaging (http://fbi.uniklinik-freiburg.de/)
Brain imaging software produced by the Brain Research Imaging Centre of The University of Edinburgh.
A collection of functions, in the end to be wrapped in a gui, that allow users to analyze networks from global (eigenvector centrality) and local (degree dist, statistical significance) perspectives. Implemented in matlab.
This project is a lab prototype of MEG default mode network in MATLAB.
Default mode network (DMN) or task negative network (TNN) may provide useful information on state of brain. Normal brain is constantly busy and demonstrates a network of synchronized activity at distinct brain regions. Trauma, injury, or resection ruptures this natural network of neuronal connectivity, subsequently altering the default scheme of synchronized activation. This utility is designed to quickly analyze and visualize the default mode network, at current state of brain, for MEG data acquired from any subject. Customization of threshold and sampling rate, followed by complete circular visualizations for quick clinical references are a plus. The program is primarily designed to facilitate clinicians, and researchers. The researchers can further analyze, if required, using the MAT file stored from the last analysis. Moreover, the framework can be used to estimate functional connectivity while performing any particular task.
This program has been written having in mind to create an useful tool to evaluate the Motor Evoked Potentials (MEPs) generated by Transcranial Magnetic Stimulation (TMS) and recorded with the program "Signal" (version 2.xx).
Probabilistic natural mapping for gene based association study.
PALM is a software that conducts gene-based association analysis. PALM exploits Hidden Markov Models (HMM) to capture the inner genomic structures. Then, unique gene features (termed "palm prints") are extracted for each gene set by calculating the natural gradient. Then palm-prints are tested with chi-square significance test.
RESCUE will be made available after publication of the PhD thesis of James Withers (Uni of Edinburgh, UK). The first version of the package will initially include super-resolution, thin structure detection, and partial volume estimation components.
These classes are useful for signal processing in Matlab or C++. They bring together tools and methods which may be used interchangeably for Matlab and C++. Their initial use is in conjunction with work towards my degree at UC Berkeley.
A matlab software platform (GUI included) for implementing literature-inspired/novel models of contrast dynamics for -- then ultimately analyzing series generated by -- the dynamic contrast-enhanced MR modality.