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http://www.nirx.net

Commercial technology solutions for NIRS neuroscience imaging applications.

Proper citation: NIRx NIRS Neuroimaging (RRID:SCR_002491) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/CFNT/index

Biomedical technology research center that develops and applies innovative neuroimaging technologies and techniques to enable closer examination of the human brain, and thereby contribute to better understanding of the brain in health and disease. They develop new techniques and advance existing technologies for acquisition and analysis of functionally specific images of the working brain, with unprecedented physiological precision and spatiotemporal resolution. The research and development aims to improve and extend existing methods for non-invasive magnetic resonance image analysis and acquisition, electromagnetic source imaging, optical neuroimaging, and most recently, combined MR-PET neuroimaging. The Resource provides an essential interactive environment, within which an interdisciplinary team of highly skilled scientists, engineers, and clinicians with diverse expertise in multiple modalities and disciplines. The resource supports service use of the Center's facilities by neuroscientists throughout the country, provide extensive training opportunities for students, fellows, and staff scientists, and seek to advance the field of brain mapping through active dissemination of new knowledge and technology.

Proper citation: Center for Functional Neuroimaging Technologies (RRID:SCR_001423) Copy   

•   Source: SciCrunch Registry

http://cng.gmu.edu/brava

A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).

Proper citation: BraVa (RRID:SCR_001407) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/collaborators/function-birn/

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

Proper citation: Function BIRN (RRID:SCR_007291) Copy   

•   Source: SciCrunch Registry

http://www.brainvisa.info/

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format

Proper citation: BrainVISA / Anatomist (RRID:SCR_007354) Copy   

•   Source: SciCrunch Registry

http://fmri.wfubmc.edu/software/PickAtlas

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy   

•   Source: SciCrunch Registry

http://mipav.cit.nih.gov

A Java-based application that enables quantitative analysis and visualization of medical images of numerous modalities such as DTI, PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV can be run on any Java-enabled platform such as Windows, UNIX, or Macintosh OS X. Functionality includes segmentation, inter- and intra multi-modality registration, surface rendering, volume rendering and reading and writing a large number of biomedical file formats including: DICOM 3.0, Analyze, NIFTI, SPM, MINC, Phillips, GE, Zeiss, Biorad, jpeg, png, tiff, mrc, fits, interfile, and many more.

Proper citation: MIPAV: Medical Image Processing and Visualization (RRID:SCR_007371) Copy   

•   Source: SciCrunch Registry

http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

•   Source: SciCrunch Registry

https://www.humanconnectome.org/software/connectome-workbench

Software brain visualization, analysis and discovery tool for fMRI and dMRI brain imaging data, including functional and structural connectivity data generated by the Human Connectome Project. Used to map brain imaging data. Allows for visualization of outputs from HCP pipelines from single subject, or average data from group of subjects and register that data onto standard brain atlas.

Proper citation: Connectome Workbench (RRID:SCR_008750) Copy   

•   Source: SciCrunch Registry

http://humanconnectome.org/

Consortium to comprehensively map long-distance brain connections and their variability. It is acquiring data and developing analysis pipelines for several modalities of neuroimaging data plus behavioral and genetic data from healthy adults.

Proper citation: Human Connectome Coordination Facility (RRID:SCR_008749) Copy   

•   Source: SciCrunch Registry

http://www.3dbar.org

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

Proper citation: 3DBar (RRID:SCR_008896) Copy   

•   Source: SciCrunch Registry

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

Open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh, Hongzhi Wang, Sandhitsu Das, Brian Avants, Philip Cook, John Pluta and Paul Yushkevich, and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.

Proper citation: AHEAD (RRID:SCR_008890) Copy   

•   Source: SciCrunch Registry

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

Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI.

Proper citation: GIFTI (RRID:SCR_009579) Copy   

•   Source: SciCrunch Registry

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

A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: DOTS WM tract segmentation (RRID:SCR_009459) 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://www.sourcesignal.com/

A technically supported modular platform for space-time-frequency analyses of EEG/MEG/ECoG integrated (optionally) with structural MRI and functional hemodynamic measures (fMRI and NIRS). The Locator module uses Polhemus devices to acquire 3D sensor coordinates. Data Editor provides pipelines of spatial and temporal filters, and easy-to-use event pipelines for conditional binning of time, frequency, and time-frequency data across participants, with group results. Coherence, phase synchronication, and quasi-causal information assess connectivity. Source Estimator enables modeling of discrete overdetermined and distributed underdetermined sources, and spatial filtering for 3D brain regions of interest. Statistical nonparametric mapping (SnPM) may be performed for all measures. MR Viewer and Image Processor comprise tools for BEM and FEM volume conductor models, using cortical source space models. See http://www.sourcesignal.com/Features_EMSE_550.pdf for details and a supported free trial.

Proper citation: EMSE Suite (RRID:SCR_009571) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/BrainParser

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/c8c8/

A small, stand-alone MatLab toolbox that measures sagittal cross-section thickness and area of the human corpus callosum from high-resolution T1 in vivo MR images. C8 takes as input affine normalized white matter segmentations derived from high-resolution (in-plane) T1 images and outputs both regional callosal thicknesses in three different formats and geometrically-defined regional areas in three different configurations. It is a small package that is easily configurable and modifiable and it measures callosa at the rate of several per minute.

Proper citation: C8: Corpus Callosum Computations (RRID:SCR_009449) Copy   

•   Source: SciCrunch Registry

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

A tutorial that took place as part of MICCAI 2010 is the 13th International Conference on Medical Image Computing and Computer Assisted Intervention, September 20-24, 2010 in Beijing, China. See http://www.miccai2010.org/ This project supporedt community outreach and dialog between presenters and audience, both before and after the tutorial session, and is intended to engage the broader community in the deliberations on this important topic. ''Best Practices'' covered software engineering practices as well end-user installation and support practices.

Proper citation: Best Practices for Software Development (RRID:SCR_009441) Copy   

•   Source: SciCrunch Registry

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

Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development.

Proper citation: Baby Brain Toolkit (RRID:SCR_009440) Copy   

•   Source: SciCrunch Registry