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

Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy.

Proper citation: Faceted Search Based Ontology Visualizer (RRID:SCR_000124) Copy   

•   Source: SciCrunch Registry

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

User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org

Proper citation: XNAT Extras (RRID:SCR_004759) Copy   

•   Source: SciCrunch Registry

http://neurolex.org/wiki/Main_Page

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

Proper citation: NeuroLex (RRID:SCR_005402) Copy   

•   Source: SciCrunch Registry

http://www2.hu-berlin.de/eyetracking-eeg

A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line.

Proper citation: EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme.

Proper citation: BRAINSTracer (RRID:SCR_012894) Copy   

•   Source: SciCrunch Registry

http://www.softpedia.com/get/Science-CAD/BrainVisa-Morphology-extensions.shtml

An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa

Proper citation: BrainVisa Morphology extensions (RRID:SCR_013248) Copy   

•   Source: SciCrunch Registry

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

An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication.

Proper citation: Generation R Pediatric MRI Resources (RRID:SCR_014114) Copy   

•   Source: SciCrunch Registry

http://enigma.ini.usc.edu/protocols/dti-protocols/

Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols.

Proper citation: ENIGMA-DTI Pipeline (RRID:SCR_014649) Copy   

•   Source: SciCrunch Registry

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

Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans.

Proper citation: DIAMOND (RRID:SCR_009457) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cbs-tools/

A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: CBS High-Res Brain Processing Tools (RRID:SCR_009452) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/hardware.cfm?ID=91

Instrument that accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant?s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed.

Proper citation: Fiber Optic Button Response System (RRID:SCR_009577) Copy   

•   Source: SciCrunch Registry

http://www.nordicneurolab.com

From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike.

Proper citation: NordicNeuroLab (RRID:SCR_009632) Copy   

•   Source: SciCrunch Registry

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

A reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields.

Proper citation: Lumina LP- 400 Response System (RRID:SCR_009596) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/diffusion-mri/

This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program, namely, Mixture of Wisharts (MOW), Diffusion Orientation Transform (DOT) and Q-ball Imaging (QBI). This program is mainly developed and maintained by Bing Jian, as part of his Ph.D. research, supervised by Prof. Baba Vemuri. Please note that the source code of this program is hosted at Google Code, see the Source Code link on the left.

Proper citation: Multi-fiber Reconstruction from DW-MRI (RRID:SCR_009509) Copy   

•   Source: SciCrunch Registry

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

This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling.

Proper citation: MASIMatlab (RRID:SCR_009506) Copy   

•   Source: SciCrunch Registry

http://www.smivision.com/en/gaze-and-eye-tracking-systems/products/iview-x-mri-meg.html

A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output

Proper citation: iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/masi-fusion/

Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided.

Proper citation: MASI Label Fusion (RRID:SCR_009505) Copy   

•   Source: SciCrunch Registry

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

Automatically creates a mask based on the "foreground" of an anatomical scan volume.

Proper citation: BRAINSROIAuto (RRID:SCR_009501) Copy   

•   Source: SciCrunch Registry

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

This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose.

Proper citation: JHU Proj. in Applied Medical Imaging (RRID:SCR_009499) Copy   

•   Source: SciCrunch Registry

http://www.vpixx.com/products/visual-stimulators/datapixx.html

Supplies a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx 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: DATAPixx (RRID:SCR_009648) Copy   

•   Source: SciCrunch Registry