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http://www.nitrc.org/projects/inia19/

Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas.

Proper citation: INIA19 Primate Brain Atlas (RRID:SCR_009498) Copy   

•   Source: SciCrunch Registry

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

A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user

Proper citation: Graphtools (RRID:SCR_009490) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/r-spit/

Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.

Proper citation: resting-state pediatric imaging template (RRID:SCR_009647) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/factory4t1ndti/

Tools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images.

Proper citation: factory t1 dti (RRID:SCR_009523) Copy   

•   Source: SciCrunch Registry

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

A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field.

Proper citation: GRETNA (RRID:SCR_009487) Copy   

•   Source: SciCrunch Registry

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

A platform for any Principal Component Analysis (PCA)-based analysis on functional neuroimaging data (PET and fMRI). Includes: * Ordinal Trend Canonical Variance Analysis for parametric designs (C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645) * Partial Least Squares for any design matrix * Subprofile Scaling Model for cross-sectional designs (JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.)

Proper citation: Generalized Covariance Analysis (RRID:SCR_009488) Copy   

•   Source: SciCrunch Registry

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

GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian, multivariate, nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis, lesion-deficit analysis, and functional MR data analysis.

Proper citation: GAMMA (RRID:SCR_009484) Copy   

•   Source: SciCrunch Registry

http://dsi-studio.labsolver.org

A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system.

Proper citation: DSI Studio (RRID:SCR_009557) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/erppcatoolkit/

This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip.

Proper citation: ERP PCA Toolkit (RRID:SCR_013105) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gsa-snp/

A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version.

Proper citation: GSA-SNP (RRID:SCR_013109) Copy   

•   Source: SciCrunch Registry

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

A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images.

Proper citation: BiofilmQuant (RRID:SCR_014088) Copy   

•   Source: SciCrunch Registry

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

Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases.

Proper citation: 7T Structural MRI scans ATAG (RRID:SCR_014084) Copy   

•   Source: SciCrunch Registry

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

A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit.

Proper citation: CAWorks (RRID:SCR_014185) Copy   

•   Source: SciCrunch Registry

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

Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer.

Proper citation: ShapePopulationViewer (RRID:SCR_014167) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/search/?type_of_search=group&q=wisconsin&sa.x=0&sa.y=0&sa=Search

Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque.

Proper citation: Rhesus Macaque Brain Atlases (RRID:SCR_017533) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/current-users/morphometry-birn/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th,2023. Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains.

Proper citation: Morphometry BIRN (RRID:SCR_000155) Copy   

•   Source: SciCrunch Registry

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

A reference MINC set of files that currently includes human head images only of standard modalities. The goal is to build a well curated collection of files that demonstrate the capabilities of MINC

Proper citation: MINC Example files (RRID:SCR_000859) Copy   

•   Source: SciCrunch Registry

http://www.temporal-lobe.com/

Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection.

Proper citation: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat (RRID:SCR_002816) Copy   

•   Source: SciCrunch Registry

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

Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.

Proper citation: Internet Brain Segmentation Repository (RRID:SCR_001994) Copy   

•   Source: SciCrunch Registry

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

Public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data.

Proper citation: Rosetta Bit (RRID:SCR_001906) Copy   

•   Source: SciCrunch Registry