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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/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/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

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

A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2.

Proper citation: freesurfR (RRID:SCR_014110) Copy   

•   Source: SciCrunch Registry

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

A multivariate method for fMRI data analysis based on generalized canonical correlation analysis (gCCA) to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. For multiple subjects, gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects.

Proper citation: gCCA (RRID:SCR_014113) Copy   

•   Source: SciCrunch Registry

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

A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results.

Proper citation: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity (RRID:SCR_014117) Copy   

•   Source: SciCrunch Registry

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

A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements.

Proper citation: HAMMER: Deformable Registration (RRID:SCR_014118) Copy   

•   Source: SciCrunch Registry

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

An MRI preprocessing pipeline built with HOF (Heterogeneous Optimization Framework) methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis in both longitudinal and cross-sectional studies. It works on DICOM images from a single MRI study and includes perfusion (DSC sequence based) analysis and DTI analysis. MGA spatially co-registers all study images to an atlas template and to a template image within the study.

Proper citation: MGA - Multimodal Glioma Analysis (RRID:SCR_014122) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/iukf_2013/

A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers.

Proper citation: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 (RRID:SCR_014127) Copy   

•   Source: SciCrunch Registry

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

A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal).

Proper citation: Turbo-BrainVoyager (RRID:SCR_014175) Copy   

•   Source: SciCrunch Registry

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

A software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project. Topographica focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. The software package provides a general-purpose framework for building models at this level, at an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation. It is intended to complement low-level neuron simulators that are available, such as General Neural Simulation System and NEURON.

Proper citation: Topographica (RRID:SCR_014174) Copy   

•   Source: SciCrunch Registry

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

A GUI-based software for real-time fMRI processing, multivoxel pattern decoding and neurofeedback. The package integrates routines for image preprocessing in real-time, ROI-based feedback and brain decoding-based feedback using the FSL and libSVM libraries. Users can create or employ pre-specified visual stimuli for neurofeedback experiments. FRIEND can be used as Windows standalone software or as a multiplatform toolbox (called FRIEND Engine).

Proper citation: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) (RRID:SCR_014186) Copy   

•   Source: SciCrunch Registry

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

A tool which implements a functional analysis pipeline for the joint analysis of longitudinally measured functional data and clinical data (for example age, gender and disease status). FMPM consists of a functional mixed effects model for characterizing the association of functional response with covariates of interest by incorporating complex spatial–temporal correlation structure, an efficient method for spatially smoothing varying coefficient functions, an estimation method for estimating the spatial– temporal correlation structure, a test procedure with local and global test statistics for testing hypotheses of interest associated with functional response, and a simultaneous confidence band for quantifying the uncertainty in the estimated coefficient functions.

Proper citation: Functional Mixed Processes Models (RRID:SCR_014187) Copy   

•   Source: SciCrunch Registry

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

A full featured and extensible application which simulates biological neural networks using graphic tools which edit neurons and networks, run the simulation and analyze results. It is written in C and runs on Unix and Windows. It is specifically targeted for neuroscientists who are less experienced with computer programming.

Proper citation: XNBC (RRID:SCR_014182) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases

Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.

Proper citation: MeshView (RRID:SCR_017222) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/dtk/

Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.

Proper citation: Diffusion Toolkit (RRID:SCR_017345) Copy   

•   Source: SciCrunch Registry

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

Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation.

Proper citation: Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) Copy   

•   Source: SciCrunch Registry

https://github.com/bheAI/MonkeyCBP_CLI

Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.

Proper citation: MonkeyCBP (RRID:SCR_017640) Copy   

•   Source: SciCrunch Registry

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

Software tool to simplify creation and management of computing environments in Neuroimaging.

Proper citation: ReproMan (RRID:SCR_018468) Copy   

•   Source: SciCrunch Registry