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

Segmentation software for multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences. Segmented tissues include Gray Matter, White Matter, Cerebrospinal Fluid, necrotic core, edema, non-enhancing tumor and enhancing tumor.

Proper citation: BraTumIA (Brain Tumor Image Analysis) (RRID:SCR_014184) 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

http://www.nitrc.org/projects/ruby-nifti/

A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby.

Proper citation: Ruby NIfTI (RRID:SCR_014164) Copy   

•   Source: SciCrunch Registry

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

A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard.

Proper citation: SCORE (RRID:SCR_014165) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pca-scalar-mesh

An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class.

Proper citation: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data (RRID:SCR_014163) Copy   

•   Source: SciCrunch Registry

http://www.angiocalc.com/

Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images.

Proper citation: AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) Copy   

•   Source: SciCrunch Registry

http://umcd.humanconnectomeproject.org

Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.

Proper citation: USC Multimodal Connectivity Database (RRID:SCR_012809) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/optseq/

Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be.

Proper citation: Optseq (RRID:SCR_014363) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gscca_2013/

Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.

Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy   

•   Source: SciCrunch Registry

http://humanconnectome.org/connectome/connectomeDB.html

Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source.

Proper citation: ConnectomeDB (RRID:SCR_004830) Copy   

•   Source: SciCrunch Registry

https://neuroscienceblueprint.nih.gov/Resources-Tools/Blueprint-Resources-Tools-Library

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.

Proper citation: Biomedical Informatics Research Network (RRID:SCR_005163) Copy   

•   Source: SciCrunch Registry

http://sig.biostr.washington.edu/projects/MindSeer/index.html

A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).

Proper citation: MindSeer (RRID:SCR_003019) Copy   

•   Source: SciCrunch Registry

Issue

https://github.com/spm

Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.

Proper citation: SPM (RRID:SCR_007037) Copy   

•   Source: SciCrunch Registry

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

Aa brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.

Proper citation: BrainNet Viewer (RRID:SCR_009446) Copy   

•   Source: SciCrunch Registry

http://cytoseg.googlecode.com

A tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. It works best for 3D blob shaped objects like mitochondria, lysosomes, etc. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools).

Proper citation: Cytoseg (RRID:SCR_009553) Copy   

•   Source: SciCrunch Registry

http://www.math.mcgill.ca/keith/surfstat

A Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory.

Proper citation: SurfStat (RRID:SCR_007081) Copy   

•   Source: SciCrunch Registry