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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   

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http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/MrDiffusion

Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MrDiffusion (RRID:SCR_016567) Copy   

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http://www.uimcimes.es/contenidos/golink?p=1

Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.

Proper citation: QModeling (RRID:SCR_016358) Copy   

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http://brainarchitecture.org/allen-atlas-brain-toolbox

Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.

Proper citation: Brain Gene Expression Analysis toolbox (RRID:SCR_017438) Copy   

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http://www.nisox.org/Software/SwE/

Software tool as SPM extension for longitudinal and repeated measures data. Modelling of longitudinal and repeated measures neuroimaging data.Implemented as Matlab toolbox for SPM8 or SPM12.

Proper citation: Sandwich Estimator Toolbox (RRID:SCR_019279) Copy   

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https://github.com/fangzcbio/DeePVP

Software tool for identification and classification of phage virion proteins using deep learning.

Proper citation: DeePVP (RRID:SCR_022474) Copy   

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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   

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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   

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https://github.com/lrq3000/auto_acpc_reorient/

Software tool as cross platform automatic AC-PC realignment,reorientation and coregistration robust to brain damage, using template matching in SPM12. Provides two new tools auto_acpc_reorient and auto_acpc_coreg using toolbox Statistical Parametric Mapping 12 to reorient and coregister structural, functional and other modalities of MRI volumetric brain images.

Proper citation: auto_acpc_reorient (RRID:SCR_018308) Copy   

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https://github.com/flatironinstitute/ironclust

Spike sorting software for multi day recordings from high channel count probes during electrophysiology experiments.

Proper citation: IronClust (RRID:SCR_018903) Copy   

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https://github.com/cochran4/GEMB

Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function.

Proper citation: GEMB (RRID:SCR_018904) Copy   

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https://github.com/treder/MVPA-Light

Software Matlab based MVPA toolbox for EEG and MEG analyses. Classification and regression toolbox for multi dimensional data. Performs cross validation, hyperparameter tuning, and nested preprocessing. Computes various classification and regression metrics and establishes their statistical significance.

Proper citation: MVPA Light (RRID:SCR_022173) Copy   

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https://github.com/fahrenfort/ADAM

Software Matlab based MVPA toolbox for EEG analyses. Allows direct comparison of ERP/ERF results to MVPA results using any dataset in standard EEGLAB or Fieldtrip format. Performs and visualizes multiple comparison corrected group decoding and forward encoding results in variety of ways, such as classifier performance across time, temporal generalization (time-by-time) matrices of classifier performance, channel tuning functions (CTFs) and topographical maps of (forward-transformed) classifier weights.

Proper citation: Amsterdam Decoding And Modeling (RRID:SCR_022172) Copy   

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https://www.ncbi.nlm.nih.gov/pubmed/23489480

Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.

Proper citation: MicroFilament Analyzer (RRID:SCR_016411) Copy   

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https://github.com/cortex-lab/Kilosort

Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.

Proper citation: KiloSort (RRID:SCR_016422) Copy   

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http://fmri.uib.no/index.php?option=com_content&view=article&id=53&Itemid=78

Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts.

Proper citation: The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) Copy   

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https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy   

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https://github.com/CPernet/brain_colours

Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.

Proper citation: Colour maps for brain imaging (RRID:SCR_016715) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

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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   

•   Source: SciCrunch Registry