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http://epilepsy.uni-freiburg.de/database

A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data.

Proper citation: EPILEPSIE database (RRID:SCR_003179) 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

https://www.nitrc.org/projects/gmac_2012/

Open-source software toolbox implemented multivariate spectral Granger Causality Analysis for studying brain connectivity using fMRI data. Available features are: fMRI data importing, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions are integrated into a graphical user interface developed in Matlab environment. Dependencies: Matlab, BIOSIG, SPM, MarsBar.

Proper citation: GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data (RRID:SCR_009581) Copy   

•   Source: SciCrunch Registry

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

An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The automated toolbox can do the following: (a1) produce identical results to the current implementation in SPM (a2) use the current implementation of PPI in SPM but using the regional mean instead of the eigenvariate (a3) use a generalized form that allows a PPI for each task to be in the same model using either the regional mean of eigenvariate (b) create the model using the output of one of the (a) options and the first level design (c) estimate the model (/results directory) (d) compute the contrasts specified.

Proper citation: Generalized PPI Toolbox (RRID:SCR_009489) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dti-denoising/

A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures.

Proper citation: DTI denoising (RRID:SCR_014102) Copy   

•   Source: SciCrunch Registry

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

A project which systematically preprocess the data from the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI) and openly share the results. Data is currently hosted in an Amazon Web Services Public S3 Bucket and at NITRC.

Proper citation: Preprocessed Connectomes Project (RRID:SCR_014162) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pd3/

THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan. 5, 2016. Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources.

Proper citation: Parkinsons Disease Discovery Database (RRID:SCR_014160) Copy   

•   Source: SciCrunch Registry

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

Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires. Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions. Is listed by Neuroimaging Informatics Tools.

Proper citation: Altered States Database (RRID:SCR_016350) Copy   

•   Source: SciCrunch Registry

http://cmic.cs.ucl.ac.uk/mig/index.php?n=Tutorial.NODDImatlab

This MATLAB toolbox implements a data fitting routine for Neurite Orientation Dispersion and Density Imaging (NODDI). NODDI is a new diffusion MRI technique for imaging brain tissue microstructure. Compared to DTI, it has the advantage of providing measures of tissue microstructure that are much more direct and hence more specific. It achieves this by adopting the model-based strategy which relates the signals from diffusion MRI to geometric models of tissue microstructure. In contrast to typical model-based techniques, NODDI is much more clinically feasible and can be acquired on standard MR scanners with an imaging time comparable to DTI.

Proper citation: NODDI Matlab Toolbox (RRID:SCR_006826) Copy   

•   Source: SciCrunch Registry

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

A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+).

Proper citation: Papaya (RRID:SCR_014188) Copy   

•   Source: SciCrunch Registry

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

A Matlab implementation for efficient permutation testing by using matrix completion.

Proper citation: Efficient Permutation Testing (RRID:SCR_014104) Copy   

•   Source: SciCrunch Registry

http://www.mouseconnectome.org/

Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse.

Proper citation: Mouse Connectome Project (RRID:SCR_004096) Copy   

•   Source: SciCrunch Registry

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

An effort to provide a set of quasi-probabilistic atlases for established functional ROIs in the human neuroimaging literature. Many atlases exist for various anatomical parcellation schemes, such as the Brodmann areas, the structural atlases, tissue segmentation atlases, etc. To date, however, there is no atlas for so-called functional ROIs. Such fROIs are typically associated with an anatomical label of some kind (e.g. the _fusiform_ face area), but these labels are only approximate and can be misleading inasmuch as fROIs are not constrained by anatomical landmarks, whether cytoarchitectonic or based on sulcal and gyral landmarks. The goal of this project is to provide quasi-probabilistic atlases for fROIs that are based on published coordinates in the neuroimaging literature. This is an open-ended enterprise and the atlas can grow as needed. Members of the neuroscience and neuroimaging community interested in contributing to the project are encouraged to do so.

Proper citation: Functional ROI Atlas (RRID:SCR_009481) Copy   

•   Source: SciCrunch Registry

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

This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The atlas includes probability maps of the Subthalamic Nucleus (STh) using T2*-imaging. For now it has been created on 13 young healthy participants with a mean age of 24.38 (range: 22-28, SD: 2.36). We recently also created atlas STh probability maps from 8 middle-aged participants with a mean age of 50.67 (range: 40-59, SD: 6.63), and 9 elderly participants with a mean age of 72.33 (range: 67-77, SD: 2.87). You can find more details about the creation of these maps in the following papers: Young: http://www.ncbi.nlm.nih.gov/pubmed/22227131 Middle-aged & Elderly: http://www.ncbi.nlm.nih.gov/pubmed/23486960 Participating institutions are the Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, and the Cognitive Science Center Amsterdam, University of Amsterdam, the Netherlands.

Proper citation: Atlasing of the basal ganglia (RRID:SCR_009431) Copy   

•   Source: SciCrunch Registry

http://iso2mesh.sourceforge.net/

A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling.

Proper citation: iso2mesh (RRID:SCR_013202) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/eprime.cfm

A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files

Proper citation: E-Prime (RRID:SCR_009567) Copy   

•   Source: SciCrunch Registry

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://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