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http://www.mazesuite.com/

A complete set of tools that enables researchers to perform spatial and navigational behavior experiments within interactive, easy to create, and extendable (e.g., multiple rooms) 3D virtual environments. MazeSuite can be used to design/edit adapted 3D environments where subjects? behavioral performance can be tracked. Maze Suite consists of three main applications; an editing program to create and alter maps (MazeMaker), a visualization/rendering module (MazeWalker), and finally an analysis/mapping tool (MazeAnalyzer). Additionally, MazeSuite has the capabilities of sending signal pulses to physiological recording devices using standard computer ports. MazeSuite, with all 3 applications, is a unique and complete toolset for researchers who want to easily and rapidly deploy interactive 3D environments. Requirements Maze Suite is designed for Windows 7, Windows Vista and Windows XP. 3D rendering quality depends on available graphics card hardware; OpenGL 2.1 or above compliant is recommended. For Windows XP systems, .NET Framework Version 2.0 or above is required and can be downloaded from Microsoft's website.

Proper citation: MazeSuite (RRID:SCR_009606) Copy   

•   Source: SciCrunch Registry

http://ric.uthscsa.edu/mango/

A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators

Proper citation: Mango (RRID:SCR_009603) Copy   

•   Source: SciCrunch Registry

http://visual.cs.utsa.edu/eegvis

A MATLAB toolbox for exploration of multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. The toolbox can be used directly in MATLAB at any stage in a user's processing pipeline, as a plug in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license. The toolbox also supplies a number of extensible base classes for users who wish to develop their own visualizations.

Proper citation: EEGVIS (RRID:SCR_009569) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/ISRNA/

An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ISRNA (RRID:SCR_009565) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/psom/

A lightweight software library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab / Octave structure. PSOM then automatically offers the following services: * Run jobs in parallel using multiple CPUs or within a distributed computing environment. * Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. * Handle job failures : successful completion of jobs is checked and failed jobs can be restarted. * Handle updates of the pipeline : change options or add jobs and let PSOM figure out what to reprocess !

Proper citation: Pipeline System for Octave and Matlab (RRID:SCR_009637) Copy   

•   Source: SciCrunch Registry

http://www.nordicneurolab.com

From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike.

Proper citation: NordicNeuroLab (RRID:SCR_009632) Copy   

•   Source: SciCrunch Registry

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

This package contains a software implementation for joint label fusion and corrective learning, which were applied in MICCAI 2012 Grand Challenge on Multi-Atlas Labeling and finished in the first place. Joint label fusion is for combining candidate segmentations produced by registering and warping multiple atlases for a target image. Corrective learning can be applied to further reduce systematic errors produced by joint label fusion. In general, corrective learning can be applied to correct systematic errors produced by other segmentation methods as well.

Proper citation: PICSL Multi-Atlas Segmentation Tool (RRID:SCR_009633) Copy   

•   Source: SciCrunch Registry

http://bisp.kaist.ac.kr/NIRS-SPM

A SPM and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. Based on the general linear model (GLM), and Sun's tube formula / Lipschitz-Killing curvature (LKC) based expected Euler characteristics, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total-hemoglobin, but also allows for super-resolution activation localization. Additional features, including a wavelet-minimum description length detrending algorithm and cerebral metabolic rate of oxygen (CMRO2) estimation without hypercapnia, were implemented in the NIRS-SPM software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NIRS-SPM (RRID:SCR_009630) Copy   

•   Source: SciCrunch Registry

http://www.cbs.mpg.de/institute/software/lipsia/

Software tool for processing functional magnetic resonance imaging (fMRI) data.Software system for evaluation of functional magnetic resonance images of human brain.

Proper citation: Lipsia (RRID:SCR_009595) Copy   

•   Source: SciCrunch Registry

http://gforge.dcn.ed.ac.uk/gf/project/limo_eeg/

A matlab toolbox (EEGlab compatible) allowing the processing of MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with the tool. Across subject analyses are performed using bootstrap offering robust inferences.

Proper citation: LIMO EEG (RRID:SCR_009592) Copy   

•   Source: SciCrunch Registry

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

This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling.

Proper citation: MASIMatlab (RRID:SCR_009506) Copy   

•   Source: SciCrunch Registry

http://www.smivision.com/en/gaze-and-eye-tracking-systems/products/iview-x-mri-meg.html

A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output

Proper citation: iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/masi-fusion/

Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided.

Proper citation: MASI Label Fusion (RRID:SCR_009505) Copy   

•   Source: SciCrunch Registry

http://itools.loni.usc.edu/

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

Proper citation: iTools (RRID:SCR_009626) Copy   

•   Source: SciCrunch Registry

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

This module reduces Rician noise on nhdr/nrrd DWIs. Filters image in mean squared error sense using Rician noise model. All estimations are performed as sample estimates in a "shaped neighborhood" defined by the weights extracted from structural similarity of voxels following same idea as in Non-Local Means filter.

Proper citation: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI (RRID:SCR_009502) Copy   

•   Source: SciCrunch Registry

http://www.cise.ufl.edu/~abarmpou/lab/fanDTasia/

A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.

Proper citation: fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/~jbm/jip/

Software toolkit for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for fMRI time series analysis, a 1st-order GLM analysis for PET data within the SRTM framework, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 4) MRI templates to place your rodent and non-human primate data into standardized spaces.

Proper citation: JIP Analysis Toolkit (RRID:SCR_009588) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/MACH/download/

QTL analysis based on imputed dosages/posterior_probabilities.

Proper citation: MACH (RRID:SCR_009621) Copy   

•   Source: SciCrunch Registry

http://www.hammersuite.com/

The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration.

Proper citation: HAMMER Suite (RRID:SCR_009583) Copy   

•   Source: SciCrunch Registry

http://econnectome.umn.edu/

An open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome La Sapienza.

Proper citation: eConnectome (RRID:SCR_009618) Copy   

•   Source: SciCrunch Registry