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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

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

This resource provides simulated DW-MRI brain images and quantitative tools for evaluating the performance of diffusion analysis methods in terms of fiber orientation estimation and false-positive/-negative fiber rates, which are of fundamental importance to tractography based studies. DW data was generated using a multi-tensor model at SNRs of 9, 18 and 36, for sets of 20, 30, 40, 60, 90 and 120 gradient directions. For each combination of SNR and gradient direction set, 10 realizations of data are provided. All data is simulated with a diffusion-weighting of b=1000, as is common for clinical acquisitions.

Proper citation: Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations (RRID:SCR_014168) Copy   

•   Source: SciCrunch Registry

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

This algorithm corrects for spikes in fMRI data, typically caused by abrupt head motion during scanning. It identifies outliers using Principal Component Analysis (PCA) in a sliding time-window; it is sensitive to global motion artifact, and stable against non-stationary signal changes.

Proper citation: SPIKECOR: fMRI tool for automated correction of head motion spikes (RRID:SCR_014169) Copy   

•   Source: SciCrunch Registry

http://www.theuais.org

A topical portal for the UAIS Lab of Lanzhou University which researches predicting depression and schizophrenia based on demographics and physiological information (EEG, ERPs, Genetics, MRI, fMRI, etc.). It also researches wearable bio-signal sensors and antennas, bio-signal processing, speech analysis, pervasive mental health, psycho-physiological computing, bioinformatics and multimodal data fusion and modeling.

Proper citation: Prediction and Diagnosis for Depression and Schizophrenia (RRID:SCR_014161) 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

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

The Longitudinal MS Lesion Imaging Archive provides Training data consisting of longitudinal images from five patients and Testing data consisting of 15 patients. Each longitudinal dataset includes T1-weighted, T2-weighted, PD-weighted, and T2-weighted FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. T1-weighted images have approximately a 1mm cubic voxel resolution, while the other scans are 1mm in plane with 3mm sections. Accounting for the multiple time points, this constitutes approximately 80 individual data sets. The Training data contains manual segmentations of the MS lesions from two different raters for each of the time points provided.

Proper citation: Longitudinal MS Lesion Imaging Archive (RRID:SCR_014136) Copy   

•   Source: SciCrunch Registry

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

Software Python tool as viewer for MRI data and numpy arrays.

Proper citation: vini: A viewer for fMRI data (RRID:SCR_017250) 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

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/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

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

Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

Proper citation: Penn Hippocampus Atlas (RRID:SCR_000421) Copy   

•   Source: SciCrunch Registry

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

Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.

Proper citation: Licensing issues in software and data (RRID:SCR_000411) Copy   

•   Source: SciCrunch Registry

http://kymata-atlas.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU).

Proper citation: Kymata Atlas (RRID:SCR_000269) Copy   

•   Source: SciCrunch Registry

http://cng.gmu.edu/brava

A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).

Proper citation: BraVa (RRID:SCR_001407) Copy   

•   Source: SciCrunch Registry

http://miriad.drc.ion.ucl.ac.uk/

A database of volumetric MRI brain-scans of 46 Alzheimer's sufferers and 23 healthy elderly people. Many scans were collected of each participant at intervals from 2 weeks to 2 years, the study was designed to investigate the feasibility of using MRI as an outcome measure for clinical trials of Alzheimer's treatments. It includes a total of 708 scans and should be of particular interest for work on longitudinal biomarkers and image analysis.

Proper citation: MIRIAD (RRID:SCR_002422) Copy   

•   Source: SciCrunch Registry