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https://github.com/hjmjohnson/DTIPrep

DTIPrep performs a Study-specific Protocol based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing.

Proper citation: DWI/DTI Quality Control Tool: DTIPrep (RRID:SCR_009562) Copy   

•   Source: SciCrunch Registry

http://www.paradigmexperiments.com

Software application for millisecond accurate experimental control for cognitive neuroscience, psychology and linguistics research. Presents text, images, sounds, movies, self-paced reading trials and rating scales. An integrated Python scripting API is available. Joystick and microphone response are available. Supports button boxes from PST, Cedrus, fORP and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Paradigm (RRID:SCR_009634) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Mach2dat:_Association_with_MACH_output

Software that performs logistic regression, using imputed SNP dosage data and adjusting for covariates.

Proper citation: Mach2dat (RRID:SCR_009599) Copy   

•   Source: SciCrunch Registry

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

Light version of the existing tool Fiber Viewer. It includes every clustering methods of Fiber Viewer such as : Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations.

Proper citation: FiberViewerLight (RRID:SCR_009476) Copy   

•   Source: SciCrunch Registry

http://www.unc.edu/~yunmli/MaCH-Admix/

A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix.

Proper citation: MaCH-Admix (RRID:SCR_009598) Copy   

•   Source: SciCrunch Registry

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

Software provided as a sub-project in the Finsler-tractography module: http://www.nitrc.org/projects/finslertract

Proper citation: Fiber-tracking based on Finsler distance (RRID:SCR_009475) Copy   

•   Source: SciCrunch Registry

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

Simple and efficient, this application performs the Weighted False Discovery Rate procedure of Benjamini and Hochberg (1997) to correct for multiple testing. The good think is that you can test virtually any number of p-values (even millions) obtained with any test-statistics for any data set. The bonus is that you can assign a-priori weights to give a better chance to those variables that you deem important. In practice, this procedure is powerful only with a relatively small number of p-values.

Proper citation: False Discovery Rate Weighted (RRID:SCR_009473) Copy   

•   Source: SciCrunch Registry

http://cis.jhu.edu/software

Software application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes. As part of these efforts the Center for Imaging Science at Johns Hopkins University developed techniques to not only compare images, but also to visualize the changes and differences. For additional information please refer to: Faisal Beg, Michael Miller, Alain Trouve, and Laurent Younes. Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision, Volume 61, Issue 2; February 2005. M.I. Miller and A. Trouve and L. Younes, On the Metrics and Euler-Lagrange Equations of Computational Anatomy, Annual Review of biomedical Engineering, 4:375-405, 2002. Software developed with support from National Institutes of Health NCRR grant P41 RR15241.

Proper citation: LDDMM (RRID:SCR_009590) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/moreinfo.php?package=BGE

A JAVA application designed to create taxonomies or hierarchies in order to classify and organize information.

Proper citation: BrainGraph Editor (RRID:SCR_009536) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

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

Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data

Proper citation: Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/gengen/

A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.

Proper citation: GenGen (RRID:SCR_013447) Copy   

•   Source: SciCrunch Registry

http://www.multifactordimensionalityreduction.org/

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

Proper citation: MDR (RRID:SCR_013427) Copy   

•   Source: SciCrunch Registry

http://www.cns.atr.jp/dni/en/downloads/brain-decoder-toolbox/

Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent.

Proper citation: Brain Decoder Toolbox (RRID:SCR_013150) Copy   

•   Source: SciCrunch Registry

http://brainbox.pasteur.fr/

Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community.

Proper citation: BrainBox (RRID:SCR_014750) Copy   

•   Source: SciCrunch Registry

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

Software tool as MRI brain segmentation system to obtain automatically volumetric brain information from RI data. Works in automatic manner and is able to provide brain structure volumes without any human interaction.

Proper citation: volBrain (RRID:SCR_021020) Copy   

•   Source: SciCrunch Registry

https://vpixx.com/products/viewpixx-3d/

VIEWPixx /3D (VPixx Technologies) is a 1920x1080 resolution, 120 Hz, calibrated research-grade LCD monitor. It is designed for stereoscopic (3D) stimulus presentation and other high-dynamic vision-science paradigms where deterministic timing and synchronized I/O are critical. It pairs fast-response industrial TN LCD glass with a custom VPixx panel/video controller and a scanning direct-RGB LED backlight engineered to reduce motion artifacts/ghosting/crosstalk, and to improve spatial uniformity, while bypassing consumer “enhancement” processing for predictable experimental output. For stereoscopic workflows, VIEWPixx /3D supports 120 Hz frame-sequential 3D (60 Hz/eye) when used with 3DPixx active shutter glasses (RF emitter + glasses kit), and it can provide a dual-link DVI console output to mirror the participant's view without adding GPU load. The system is also a synchronized display + acquisition toolbox: integrated button-box interface, 24-channel TTL triggers, stereo audio I/O, and a full analog I/O subsystem are implemented on the same board as video control to enable microsecond-precision synchronization to video refresh—useful for EEG triggers, reaction-time tasks, and other timing-sensitive paradigms.In terms of bit depth, the VIEWPixx /3D is native 8 bits per colour, with support fot 10-bit resolution per RGB channel via custom video modes.

Proper citation: VPixx: VIEWPixx /3D (RRID:SCR_009646) Copy   

•   Source: SciCrunch Registry

http://www.cns.atr.jp/dni/en/downloads/tools-for-brain-behavior-data-sharing/

This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file.

Proper citation: Matlab Neuroshare Library (RRID:SCR_006957) Copy   

•   Source: SciCrunch Registry

http://www.neuroconstruct.org/

Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.

Proper citation: neuroConstruct (RRID:SCR_007197) Copy   

•   Source: SciCrunch Registry

http://www.rogue-research.com

Neuronavigation system for use in human cognitive neuroscience (TMS, EEG, NIRS) and for non-human neurosurgical applications.

Proper citation: Brainsight (RRID:SCR_009539) Copy   

•   Source: SciCrunch Registry