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https://www.nitrc.org/projects/metalab_gtg/

A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times.

Proper citation: Graph Theory GLM (GTG) MATLAB Toolbox (RRID:SCR_014075) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/bic-mni-models/

Anatomical brain template library which includes models from ICBM 2009 template.Number of unbiased non-linear averages of MNI152 database have been generated that combines attractions of both high-spatial resolution and signal-to-noise while not being subject to vagaries of any single brain. Procedure involved multiple iterations of process where, at each iteration, individual native MRIs were non-linearly fitted to the average template from previous iteration, beginning with MNI152 linear template.

Proper citation: bic-mni-models (RRID:SCR_014087) Copy   

•   Source: SciCrunch Registry

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

A tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field, a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Other key features include: view synchronization, adjustable mesh resolution, and conversion from deformation and HAMMER displacement fields.

Proper citation: Displacement Field Viewer (RRID:SCR_014101) Copy   

•   Source: SciCrunch Registry

http://treestoolbox.org/

Software package, written in Matlab (Mathworks, Natick, MA), providing tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees. It provides the basic tools to edit, visualize and analyze dendritic and axonal trees, methods for quantitatively comparing branching structures between neurons, and tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.

Proper citation: TREES toolbox (RRID:SCR_010457) Copy   

•   Source: SciCrunch Registry

http://www.harvard.edu/

Institution of higher education in the United States. Private Ivy League research university in Cambridge, Massachusetts.

Proper citation: Harvard University; Cambridge; United States (RRID:SCR_011273) Copy   

•   Source: SciCrunch Registry

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

A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface.

Proper citation: Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) Copy   

•   Source: SciCrunch Registry

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

A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications.

Proper citation: libSBML (RRID:SCR_014134) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mrml-paraview/

ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView.

Proper citation: KWScene: MRML-based Atlas and Scene Builder/Reader/Writer (RRID:SCR_014131) Copy   

•   Source: SciCrunch Registry

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

Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods.

Proper citation: MARS (Multi-Atlas Robust Segmentation) (RRID:SCR_014137) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/minc-toolkit

A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp.

Proper citation: minc-toolkit (RRID:SCR_014138) Copy   

•   Source: SciCrunch Registry

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

A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior.

Proper citation: Neoseg (RRID:SCR_014144) Copy   

•   Source: SciCrunch Registry

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

This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results.

Proper citation: NeoSegPipeline (RRID:SCR_014145) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/neuron-c/

A simulation language for modeling biophysically realistic neural circuits (1 to 10,000 neurons) and simulating physiology experiments on it. Programs for plotting and displaying data are included.

Proper citation: Neuron-C (RRID:SCR_014148) Copy   

•   Source: SciCrunch Registry

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

A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.

Proper citation: NIH Pediatric MRI Data Repository (RRID:SCR_014149) Copy   

•   Source: SciCrunch Registry

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

A practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. It is designed for diffusion MRI researchers who are interested in understanding and developing diffusion pulse sequences for imaging microstructure.

Proper citation: MISST - Microstructure Imaging Sequence Simulation ToolBox (RRID:SCR_014140) Copy   

•   Source: SciCrunch Registry

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

A tool which offers a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units (GPUs). The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data.

Proper citation: Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation (RRID:SCR_014108) Copy   

•   Source: SciCrunch Registry

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

A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included.

Proper citation: Forward: Accurate finite element electromagnetic head models (RRID:SCR_014109) Copy   

•   Source: SciCrunch Registry

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

A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain.

Proper citation: ERPwavelab (RRID:SCR_014106) Copy   

•   Source: SciCrunch Registry

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

A functional connectivity analysis tool for near-infrared spectroscopy data. Its functions include preprocessing, quality control, FC calculation and network analysis.

Proper citation: Functional Connectivity Analysis Tool for near-infrared spectroscopy data (RRID:SCR_014111) Copy   

•   Source: SciCrunch Registry

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

A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment.

Proper citation: GazeReader (RRID:SCR_014112) Copy   

•   Source: SciCrunch Registry