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

Software tool for MRI intensity standardization by aligning histograms of higher dimensions. The methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf are implemented as and ITK filter.

Proper citation: VectorValuedHistogramNormalizer (RRID:SCR_000082) Copy   

•   Source: SciCrunch Registry

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

This resouce will centralize development of tools for interaction with medical imaging data in immersive virtual environments (based on the Vizard platform).

Proper citation: Medical Image Processing and Visualization in Virtual Environments (RRID:SCR_001751) Copy   

•   Source: SciCrunch Registry

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

Based on JIST and MIPAV, this pipeline combines structural magnetic resonance data with diffusion tensor imaging to estimate a connectome, which is a comprehensive description of the wiring diagram of the brain.

Proper citation: MR Connectome Automated Pipeline (RRID:SCR_002252) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

•   Source: SciCrunch Registry

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

An EEGLAB plugin which adaptively estimates and removes sinusoidal artifacts from independent component analysis (ICA) components or scalp channels using a frequency-domain (multi-taper) regression technique with a Thompson F-statistic for identifying significant sinusoidal artifacts. This approach has been advocated by Partha Mitra and Hemant Bokil (Observed Brain Dynamics, Chapter 7.3.4., 2007) and CleanLine utilizes modified routines from the Mitra Lab's Chronux Toolbox (www.chronux.org). Sinusoidal noise can be a prominent artifact in recorded electrophysiological data. This can stem from AC power line fluctuations (e.g. 50/60 Hz line noise + harmonics), power suppliers (e.g. in medical equipment), fluorescent lights, etc. Notch filtering is generally undesirable due to creation of band-holes, and significant distortion of frequencies around the notch frequency (as well as phase distortion at other frequencies and Gibbs rippling in the time-domain).

Proper citation: CleanLine (RRID:SCR_002233) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/hardware.cfm?ID=92

MRI Simulator that provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children, the elderly, and psychiatric patients, are often prone to claustrophobia and anxiety in the bore of a magnet, and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5%, improving cost effectiveness.

Proper citation: PST MRI Simulator (RRID:SCR_002460) Copy   

•   Source: SciCrunch Registry

http://www.brain.org.au/software/

A collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them. Its primary use is to enable the testing of tracking algorithms

Proper citation: Numerical Fibre Generator (RRID:SCR_002457) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/hardware.cfm?ID=90

MRI Digital Projection System that uses Digital Light Processing (DLP) technology providing microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images. Includes: * High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor * Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room * 30 meter fiber optic cable that runs between the projector and projector control station * Heavy duty, magnet compatible, projector stand (assembly required) * Heavy duty, magnet compatible mirror stand with mirror (assembly required) * High resolution, lenticular pitch rear projection screen for high quality image reproduction * Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended)

Proper citation: MRI Digital Projection System (RRID:SCR_002486) Copy   

•   Source: SciCrunch Registry

http://mousetracker.jbfreeman.net

A free, user-friendly software package that allows researchers to record and analyze hand movements traveling toward potential responses on the screen (via the x, y coordinates of the computer mouse). By looking at the dynamics of how participants' hand movements settle into a response alternative--and how they may be partially pulled toward other alternatives--researchers glean valuable information about real-time cognitive processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. MouseTracker has impressive temporal resolution, comparable to eye-tracking and event-related brain potential (ERP) measures. Experiments can incorporate images, letter strings, sounds, and videos. Once recorded, mouse trajectories can be visualized, averaged, and explored, and measures of attraction/curvature, complexity, velocity, and acceleration can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, cognitive science, and beyond.

Proper citation: MouseTracker (RRID:SCR_005979) Copy   

•   Source: SciCrunch Registry

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

A macaque brain MRI database characterizing the normal postnatal macaque brain development. This longitudinal primate database was acquired from a cohort of healthy macaque monkeys ranging from a few week olds up to 3-year-old adolescents. Each scan consists of structural (both T1 and T2) and diffusion MRI.

Proper citation: UNC-Wisconsin Neurodevelopment Rhesus MRI Database (RRID:SCR_014177) Copy   

•   Source: SciCrunch Registry

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

This algorithm corrects for spikes in fMRI data, typically caused by abrupt head motion during scanning. It identifies outliers using Principal Component Analysis (PCA) in a sliding time-window; it is sensitive to global motion artifact, and stable against non-stationary signal changes.

Proper citation: SPIKECOR: fMRI tool for automated correction of head motion spikes (RRID:SCR_014169) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/asl_spm8/

Quick ASL Wrapper for preprocessing arterial spin labeled (ASL) Data and computing blood flow measurements using UPenn ASL toolbox.

Proper citation: ASL spm8 (RRID:SCR_008873) Copy   

•   Source: SciCrunch Registry

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

An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data.

Proper citation: ANTsR (RRID:SCR_008891) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSConstellationDetector

This program will find the mid-sagittal plane, the AC, PC, and mpj points in an image, and create an AC/PC aligned data set with the AC point at the center of the voxel lattice (la beled at the origin of the image physical space.) This work is an extention of the algorithms originally described by Dr. Babak A. Ardekani, Alvin H. Bachman, Model-based automatic detection of the anterior and posterior commissures on MRI scans, N euroImage, Volume 46, Issue 3, 1 July 2009, Pages 677-682, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2009.02.030. (http://www.sciencedirect.com/science/article/B6WNP-4VRP25C-4/2/8207b962a38aa83c822c6379bc43fe4c)

Proper citation: BRAINSConstellationDetector (RRID:SCR_012856) Copy   

•   Source: SciCrunch Registry

http://vpixx.com/products/visual-stimulus-displays/viewpixx.html

A complete display toolbox which has been conceived specifically to replace CRTs in vision science labs. The VIEWPixx features high-performance industrial LCD glass, and a panel controller which has been custom designed to support vision research.Our innovative LED backlight design features superior display uniformity, and a wide color gamut exceeding that of any CRT. In addition, it includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision.

Proper citation: VIEWPixx (RRID:SCR_013271) Copy   

•   Source: SciCrunch Registry

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

A web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner.

Proper citation: Cerebral Blood Flow Database and Analysis Pipeline (RRID:SCR_009454) Copy   

•   Source: SciCrunch Registry

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

Software package that provides 3D imaging resources such as multimodal imaging, volume and mesh processing or segmentation for Dental Research. DentalTools package intends to contribute to the free exchange of information and methods in the dentistry research community.

Proper citation: DentalTools (RRID:SCR_009463) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/caGWAS/caGWAS

Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data.

Proper citation: caGWAS (RRID:SCR_009617) Copy   

•   Source: SciCrunch Registry

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

Infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware.

Proper citation: NeuroWeb - NeuroImaging Database (RRID:SCR_009610) Copy   

•   Source: SciCrunch Registry

http://www.magventure.com

A complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry.

Proper citation: MagPro Magnetic Stimulator (RRID:SCR_009601) Copy   

•   Source: SciCrunch Registry