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http://www.nitrc.org/projects/vmas_2020/

Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics.

Proper citation: Ventricular Morphometry Analysis System (RRID:SCR_019007) Copy   

•   Source: SciCrunch Registry

https://github.com/cwatson/braingraph/

Software R package for performing graph theory analyses of brain MRI data.

Proper citation: brainGraph (RRID:SCR_017260) Copy   

•   Source: SciCrunch Registry

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

Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.

Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/uf2c/

Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters.

Proper citation: User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) Copy   

•   Source: SciCrunch Registry

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

MATLAB Toolbox which provides a mixed effect model for gene-environment interaction (MixGE) on neuroimaging phenotypes, such as structural volumes and tensor-based morphometry (TBM). This model incorporates both fixed and random effects of genetic-set and environment interaction in order to investigate homogeneous and heterogeneous contributions of sets of genetic variants and their interactions with environmental risks to phenotypes.

Proper citation: Mixed Effect Model of Genetic-Set and Environment Interaction (RRID:SCR_015514) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/optseq/

Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be.

Proper citation: Optseq (RRID:SCR_014363) 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/gscca_2013/

Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.

Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/viste/

Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is supported. HARDI data is interactively visualized using highly detailed glyphs rendered on the GPU. HARDI glyphs can be visualized in combination with DTI glyphs, for a better overview of complex diffusion data. * vIST/e includes support for NVIDIA's Compute Unified Device Architecture (CUDA), which enables highly parallel, GPU-based data processing, allowing for significant speed-up of computationally expensive algorithms.

Proper citation: vIST/e (RRID:SCR_001627) Copy   

•   Source: SciCrunch Registry

http://coins.mrn.org/

A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user intervention. The database also offers scan annotation and behavioral data management, radiology review event reports, and scan time billing. * Assessment Data Collection: Clinical data gathered from interviews, questionnaires, and neuropsychological tests are entered into COINS through the web application called Assessment Manager (ASMT). ASMT's intuitive design allows users to start data collection with little or no training. ASMT offers several options for data collection/entry: dual data entry, for paper assessments, the Participant Portal, an online tool that allows subjects to fill out questionnaires, and Tablet entry, an offline data entry tool. * Data Sharing: De-identified neuroimaging datasets with associated clinical-data, cognitive-data, and associated meta-data are available through the COINS Data Exchange tool. The Data Exchange is an interface that allows investigators to request and share data. It also tracks data requests and keeps an inventory of data that has already been shared between users. Once requests for data have been approved, investigators can download the data directly from COINS.

Proper citation: Mind Research Network - COINS (RRID:SCR_000805) Copy   

•   Source: SciCrunch Registry

https://github.com/QMICodeBase/TORTOISEV4

An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.

Proper citation: TORTOISE (RRID:SCR_001645) Copy   

•   Source: SciCrunch Registry

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

VUIIS (Vanderbilt University Institute of Imaging Science) Image and Data Analysis Core's data processing tools written for MATLAB and, unless stated otherwise, capable of processing 2D/3D images (matrices). These tools are written for ease of use from within MATLAB.

Proper citation: vuTools (RRID:SCR_001704) Copy   

•   Source: SciCrunch Registry

http://www.mbfbioscience.com/neurolucida

Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Workstation. The Standard version enables control of microscope hardware, whereas the Workstation version is used for offline analysis away from the microscope. Neurolucida provides quantitative analysis with results presented in graphical or spreadsheet format exportable to Microsoft Excel. Overall, features include: - Tracing Neurons - Anatomical Mapping - Image Processing and Analysis Features - Editing - Morphometric Analysis - Hardware Integration - Cell Analysis - Visualization Features Sponsors: Neurolucida is supported by MBF Bioscience.

Proper citation: Neurolucida (RRID:SCR_001775) Copy   

•   Source: SciCrunch Registry

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

Software tool as MRI brain segmentation system to obtain automatically volumetric brain information from RI data. Works in automatic manner and is able to provide brain structure volumes without any human interaction.

Proper citation: volBrain (RRID:SCR_021020) Copy   

•   Source: SciCrunch Registry

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

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

Proper citation: Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) Copy   

•   Source: SciCrunch Registry

http://micro-manager.org

Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

Proper citation: uManager (RRID:SCR_000415) Copy   

•   Source: SciCrunch Registry

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

Scribe encodes papers to populate the BrainMap Database

Proper citation: Scribe (RRID:SCR_000423) Copy   

•   Source: SciCrunch Registry

http://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

•   Source: SciCrunch Registry

http://www.talairach.org/

Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.

Proper citation: Talairach Daemon (RRID:SCR_000448) Copy   

•   Source: SciCrunch Registry

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

Autism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach and education The ATP is not a clinical organ procurement agency, but rather they facilitate the wishes of donors and families to donate their tissue to autism research. Through the ATP's established international infrastructure, they work with any accredited tissue bank, organ procurement agency, or medical examiner that receives a family's request to donate their loved one's tissue to the program. Once contacted, the ATP will insure that the family's request to donate their loved one's tissue is faithfully met, covering all costs to the family and partnering agency as well as ensuring the tissues' proper and rapid transport to the ATP's repository at the Harvard Brain Tissue Resource Center (HBTRC) in Boston, Massachusetts.

Proper citation: Autism Tissue Program (RRID:SCR_000651) Copy   

•   Source: SciCrunch Registry