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http://www.nitrc.org/projects/nitrc

NITRC-wide community facilities: Forums, Wiki, Tracker, and News.

Proper citation: NITRC Community (RRID:SCR_009631) Copy   

•   Source: SciCrunch Registry

http://itools.loni.usc.edu/

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

Proper citation: iTools (RRID:SCR_009626) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/MACH/download/

QTL analysis based on imputed dosages/posterior_probabilities.

Proper citation: MACH (RRID:SCR_009621) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vmagnotta/

A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools

Proper citation: GTRACT (RRID:SCR_009651) Copy   

•   Source: SciCrunch Registry

http://www.restfmri.net

A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files.

Proper citation: REST: a toolkit for resting-state fMRI (RRID:SCR_009641) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/qcqp/

Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction.

Proper citation: QCQP (RRID:SCR_009640) Copy   

•   Source: SciCrunch Registry

http://beast.bio.ed.ac.uk/

A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Proper citation: BEAST (RRID:SCR_010228) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/iterdrwsp/

Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization.

Proper citation: Iterative dual-regression with sparse prior (RRID:SCR_014128) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cmind_py_2014/

A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project.

Proper citation: CMIND PY (RRID:SCR_014097) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/neuritetracer

A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons.

Proper citation: NeuriteTracer (RRID:SCR_014146) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/bvqxtools

A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab.

Proper citation: NeuroElf (RRID:SCR_014147) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/exposition/

An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition.

Proper citation: ExPosition Packages (RRID:SCR_014107) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/biomag_group/

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG).

Proper citation: Biomag Discussion Group on Yahoo (RRID:SCR_014089) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hdbig/

A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association.

Proper citation: HDBIG (RRID:SCR_014120) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/aperture/

A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures.

Proper citation: APERTURE (RRID:SCR_014082) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/openvibe

A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time.

Proper citation: OpenViBE (RRID:SCR_014156) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nusdast

A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.

Proper citation: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/openwalnut/

Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows.

Proper citation: OpenWalnut (RRID:SCR_014157) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/csa-odf

A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI.

Proper citation: Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (RRID:SCR_014158) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/niistat/

A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data.

Proper citation: NiiStat (RRID:SCR_014152) Copy   

•   Source: SciCrunch Registry