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http://www.mathworks.com/products/matlab/
Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.
Proper citation: MATLAB (RRID:SCR_001622) Copy
STRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation.
Proper citation: Spatio- Spectro- Temporal Receptive Field (RRID:SCR_007995) Copy
http://www.loni.usc.edu/Software/MultiPhase-SEG
A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed.
Proper citation: MultiPhase-SEG (RRID:SCR_008275) Copy
http://neuroimage.usc.edu/brainstorm/
Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.
Proper citation: Brainstorm (RRID:SCR_001761) Copy
Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.
Proper citation: MNE software (RRID:SCR_005972) Copy
http://www.cma.mgh.harvard.edu/iatr/display.php?spec=id&ids=107
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community.
Proper citation: Extensible MATLAB Medical image Analysis (RRID:SCR_013499) Copy
https://www.fieldtriptoolbox.org
Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.
Proper citation: FieldTrip (RRID:SCR_004849) Copy
https://github.com/automaticanalysis/automaticanalysis
Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.
Proper citation: Automatic Analysis (RRID:SCR_003560) Copy
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
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
http://www.cse-lab.ethz.ch/index.php?&option=com_content&view=article&id=363
Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Tscratch (RRID:SCR_014282) Copy
A multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave. Links to examples, exercises, and information for developers are available on the main page.
Proper citation: CoSMoMVPA (RRID:SCR_014519) Copy
https://uk.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.
Proper citation: Tools for NIfTI and ANALYZE image (RRID:SCR_016895) Copy
https://github.com/ICB-DCM/PESTO
Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.
Proper citation: PESTO (RRID:SCR_016891) Copy
http://cqb.pku.edu.cn/ZhuLab/PPR_Meta
Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PPR-Meta (RRID:SCR_016915) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.
Proper citation: PALM (RRID:SCR_017029) Copy
https://github.com/neitzlab/sbfsem-tools
Data analysis and 3D visualization for connectomics and serial electron microscopy. This toolbox provides missing 3D visualization and analysis tools for cylinder-based annotations. Integration with contour, skeleton based annotations and common morphology file formats is also supported.
Proper citation: SBFSEM-tools (RRID:SCR_017350) Copy
https://www.cmrr.umn.edu/downloads/mrspa
Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.
Proper citation: MRspa (RRID:SCR_017292) Copy
A Matlab adapter class and user interface to control the Reglo ICC peristaltic pump provided by Ismatec.
Proper citation: Reglo ICC control with Matlab (RRID:SCR_016353) Copy
Software for empirical gramians for model reduction of (nonlinear) input-output systems.
Proper citation: Empirical Gramian Framework (RRID:SCR_015043) Copy
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