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

Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.

Proper citation: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) Copy   

•   Source: SciCrunch Registry

http://signalml.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An XML-based language designed for metadescription of formats, used for digital storage of biomedical time series. Using SignalML, information on the structure of binary data files can be simply and efficiently coded. Once written, this information can be used by any software, which - owing to this metadescription - can read data files in the original format. This eliminates the need for conversions and duplication of data. signalml.org provides the following resources for interchange of relevant information and ideas: * SignalML wiki * Newsgroup / mailing list The main current software project is Svarog - a SignalML-compliant signal viewer, annotator, analyzer and (future) recorder. Svarog is written in Java and is currently best fitted for display of EEG and MEG signals. Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.

Proper citation: signalml.org (RRID:SCR_003383) Copy   

•   Source: SciCrunch Registry

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

A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.

Proper citation: NIH Pediatric MRI Data Repository (RRID:SCR_014149) Copy   

•   Source: SciCrunch Registry

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

A multivariate method for fMRI data analysis based on generalized canonical correlation analysis (gCCA) to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. For multiple subjects, gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects.

Proper citation: gCCA (RRID:SCR_014113) Copy   

•   Source: SciCrunch Registry

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

A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times.

Proper citation: Graph Theory GLM (GTG) MATLAB Toolbox (RRID:SCR_014075) Copy   

•   Source: SciCrunch Registry

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

Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data.

Proper citation: MultiXplore (RRID:SCR_014814) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu//abecasis/MACH/index.html

A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Proper citation: MACH 1.0 (RRID:SCR_001759) Copy   

•   Source: SciCrunch Registry

http://erpinfo.org/erplab

A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH.

Proper citation: ERPLAB (RRID:SCR_009574) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/trac/OpenElectrophy

Software Python module for electrophysiology data analysis.

Proper citation: OpenElectrophy (RRID:SCR_000819) Copy   

•   Source: SciCrunch Registry

http://brainproducts.com/productdetails.php?id=17

Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.

Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy   

•   Source: SciCrunch Registry

http://rtimage.sourceforge.net/

Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data.

Proper citation: RT Image (RRID:SCR_002535) Copy   

•   Source: SciCrunch Registry

http://www.neurobs.com/

Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures.

Proper citation: Presentation (RRID:SCR_002521) Copy   

•   Source: SciCrunch Registry

http://sites.google.com/site/marcocongedo/software/nica

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99.

Proper citation: Normative Independent Component Analysis (RRID:SCR_002506) Copy   

•   Source: SciCrunch Registry

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

High quality data, open and freely available to everyone to celebrate the diversity of the vertebrate brain. Do you have data that you would like to share? Do not hesitate to contact them! The Brain Catalogue is developed by Florencia Grisanti (Taxidermy Workshop of the Natural History Museum in Paris) and Roberto Toro (Neuroscience Department of the Institut Pasteur). Many of our specimens come from the Vertebrate Brain Collection of the Jardin des Plantes, curated by Marc Herbin, and are scanned at the Institut du Cerveau et de la Moelle (ICM) by Mathieu Santin and Alexandra Petiet, from the CENIR laboratory, with financial and methodological support kindly provided by Olivier Colliot, head of the Cogimage team at the ICM.

Proper citation: Brain Catalogue (RRID:SCR_009442) Copy   

•   Source: SciCrunch Registry

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

A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used.

Proper citation: Multivariate General Linear Models (MGLM) on Riemannian Manifolds (RRID:SCR_014143) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/dtk/

Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.

Proper citation: Diffusion Toolkit (RRID:SCR_017345) Copy   

•   Source: SciCrunch Registry

http://physics.ucsd.edu/neurophysics/links.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, analysis program MPView and several software utilities.

Proper citation: MPScope (RRID:SCR_000065) Copy   

•   Source: SciCrunch Registry

http://cogpo.org

Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response.

Proper citation: Cognitive Paradigm Ontology (RRID:SCR_002235) Copy   

•   Source: SciCrunch Registry

http://www.jeiglesias.com

An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts.

Proper citation: ROBEX (RRID:SCR_002534) Copy   

•   Source: SciCrunch Registry

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

A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial.

Proper citation: REX (RRID:SCR_002532) Copy   

•   Source: SciCrunch Registry