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http://cibsr.stanford.edu/tools/human-brain-project/artrepair-software.html

A toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment, data repair, and noise filtering, and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data, including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change. * Operating System: OS Independent * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 * execution requires: SPM

Proper citation: ArtRepair for robust fMRI (RRID:SCR_005990) 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://free-d.versailles.inra.fr/html/freed.html

Free-D allows the reconstruction of 3D models from image stacks (segmentation, registration, surface reconstruction, 3D rendering). It is designed in the goal of non-linear spatial normalization and averaging of collections of individual 3D models (this module is currently in alpha version only and not included in the distributed version)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Free-D (RRID:SCR_009578) Copy   

•   Source: SciCrunch Registry

http://musc.edu/cbi/dki

A software tool for post-processing diffusional kurtosis imaging (DKI) datasets. DKE consists of a suite of command-line programs along with a graphical user interface (GUI). DKE is currently supported on 32- and 64-bit Windows platforms. Given a set of diffusion-weighted images acquired following a valid DKI protocol, DKE generates a set of kurtosis (axial, mean, radial) parametric maps. DKE also generates diffusivity (axial, mean, radial) and fractional anisotropy maps using both DKI and diffusion tensor imaging signal models. DKE features include: DICOM and NIfTI format support, interactive (GUI) as well as batch mode (command-line) processing, and rigid-body motion correction. DKE implements the methods described in the following paper: Tabesh A, Jensen JH, Ardekani BA, and Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Mag Reson Med. 2011 Mar;65(3):823-36. http://www.ncbi.nlm.nih.gov/pubmed/21337412

Proper citation: Diffusional Kurtosis Estimator (RRID:SCR_009563) Copy   

•   Source: SciCrunch Registry

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

An on-line tutorial on how to use MATLAB for Diffusion-Weighted MRI processing. The following subjects are covered in this tutorial: Generation of Synthetic Diffusion-Weighted MRI datasets, Diffusion Tensor (DTI) Estimation from DW-MRI, DTI Visualization as a field of ellipsoids, Higher-order Diffusion Tensor Estimation from DW-MRI, Computing of Tensor Orientation Distribution Functions (Tensor ODF), Computing of Fiber Orientations, Higher-order Diffusion Tensor Image Visualization as fields of spherical functions, Multi-fiber reconstruction etc. The tutorial contains numerous illustrations, figures and Matlab scripts embedded in the text. The reader/user can automatically generate Matlab script for a self-designed DW-MRI experiment by selecting which steps needs to be followed. The code that corresponds to the selected steps is then appropriately merged in the Matlab Script Generator, and the user can easily copy and paste the produced code directly to the Matlab command prompt.

Proper citation: MATLAB Tutorial on Diffusion Tensor MRI (RRID:SCR_009507) Copy   

•   Source: SciCrunch Registry

http://neurospaces.sourceforge.net/

The GEneral NEural SImulation System (GENESIS) started as a very advanced software package in the late eighties, for biologically accurate neuronal modeling. Besides being used as a neuronal simulator, it was also applied to various domains outside computational neuroscience. The Neurospaces project is a departure from the monolithic software system design of the original GENESIS system. It is a development center for software components of computational neuroscience simulators. There are many advantages of developing independent software components: - Interfacing to an individual component is obviously more simple than interfacing to a do-all monolithic system. The compartmental solver developed for the Neurospaces project can be connected to Matlab fi. - It simplifies the individual components and encourages other developers to get involved. - It allows for separate testing of the components. More than 1000 use case tests been defined for these software components, including integration tests. - Integrating different component, gives different flavours of the same simulator, and enhances the user experienced consistency when doing multilevel simulations. - A component based software system avoids vendor-lockin. Its life-cycle is more smooth than that of a monolithic system, because software components can be upgraded one at a time. The Neurospaces project embodies many software components that all have been developed in full isolation. The core of the most important components is finished. The current development focus has shifted from component integration to the support of specific use case with an emphasis on single neuron modeling. This is a list of software components that have been developed or are under construction. Together, these tools give the core for the upcoming GENESIS 3 GUI. - GShell: a simple replacement for the Genesis 2 SLI. - Heccer: a fast compartmental solver, a backend. - Dash: a second compartmental solver faster than Heccer, for simpler models. - Neurospaces Model Container: provides a solver independent internal and external storage format for models. - Discrete event system: consists of a discrete event distributor and queuer. This is used for abstract modeling of an action potential traveling inside an axon as a ''discrete event''. - SSP: a flexible scheduler written in perl, to run simulations with the Neurospaces model container and Heccer. - The Neurospaces Studio: some tools for graphical browsing and command line usage. - The Genesis Script Language Interface: a scripting component that reads Genesis 2 scripts and feeds them to the Neurospaces model container. - The Geometry Library is a general purpose geometry library, with some essential geometrical operators, not commonly found in other geometrical libraries. - Using the Geometry Library, a Reconstruct Interface has been written. This interface supports the conversion of contours exported by the Reconstruct software to the Neurospaces declarative NDF format. - The Neurospaces project browser for browsing projects and inspecting simulation results. - The Installer package contains the Neurospaces installer and developer tools that have emerged from developing Neurospaces software components. - The Configurator package contains configuration utilities for the other tools. It is not needed for the other tools to work properly. Rather, it allows to set up model database and simulation servers in a convenient way. - There is also a Neurospaces blog and a wiki at googlecode for the Neurospaces project, with information for developers.

Proper citation: GEneral NEural SImulation System: The Neurospaces Project (RRID:SCR_008035) Copy   

•   Source: SciCrunch Registry

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

A GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level.

Proper citation: CARLsim: a GPU-accelerated SNN Simulator (RRID:SCR_014095) Copy   

•   Source: SciCrunch Registry

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

A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.

Proper citation: MRIcroS (RRID:SCR_014142) Copy   

•   Source: SciCrunch Registry

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

A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used.

Proper citation: Multivariate General Linear Models (MGLM) on Riemannian Manifolds (RRID:SCR_014143) Copy   

•   Source: SciCrunch Registry

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

Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.

Proper citation: GIMME (RRID:SCR_014115) Copy   

•   Source: SciCrunch Registry

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

A set of many useful automation scripts to facilitate the neuroimaging data analysis process. It contains BASH scripts for MRI data management, FSL automation and web application.

Proper citation: XFSL: An FSL toolbox (RRID:SCR_014181) Copy   

•   Source: SciCrunch Registry

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

Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools.

Proper citation: Parallel Stochastic Ion Channel Simulator (RRID:SCR_014159) 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/reproman/

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

Proper citation: ReproMan (RRID:SCR_018468) 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

https://scicrunch.org/scicrunch/data/source/nlx_154697-10/search?q=*&l=

A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).

Proper citation: Integrated Software (RRID:SCR_004745) 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