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https://github.com/cwatson/braingraph/
Software R package for performing graph theory analyses of brain MRI data.
Proper citation: brainGraph (RRID:SCR_017260) Copy
http://www.brainimagelibrary.org
Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets.
Proper citation: Brain Image Library (RRID:SCR_017272) Copy
https://github.com/Mark-Kramer/Seizure-Waves
Analysis and modeling code for waves of seizure activity.
Proper citation: Seizure-Waves (RRID:SCR_017455) Copy
Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.
Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy
https://www.ibis-network.org/index.html
Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers
Proper citation: IBIS Network (RRID:SCR_017399) Copy
Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
Proper citation: NeMO Analytics (RRID:SCR_018164) Copy
http://mialab.mrn.org/index.html
MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition.
Proper citation: MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) Copy
http://www.brain-map.org/api/index.html
API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service
Proper citation: Allen Brain Atlas API (RRID:SCR_005984) Copy
A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications.
Proper citation: Viking Viewer for Connectomics (RRID:SCR_005986) Copy
http://www.nitrc.org/projects/abc
A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.
Proper citation: ABC (Atlas Based Classification) (RRID:SCR_005981) Copy
http://www.fmriconsulting.com/brodmann/
An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded.
Proper citation: Brodmann's Interactive Atlas (RRID:SCR_006368) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project to advance understanding of the neural mechanisms of vocal learning by providing a quantitative description of the relationship between physiological variables and vocal performance over the course of development in a songbird, the zebra finch. They propose to study vocal learning dynamically across neuronal and peripheral subsystems, using a novel collaborative approach that will harness the combined expertise of several investigators. Their proposed research model will 1) provide simultaneous measurements of acoustic, articulatory and electrophysiological data that will document the detailed dynamics of the vocal imitation process in a standardized learning paradigm; and 2) incorporate these measurements into a theoretical/computational framework that simultaneously provides a phenomenological description and attempts to elucidate the mechanistic basis of the learning process.
Proper citation: Zebra Finch Song Learning Consortium (RRID:SCR_006356) Copy
http://brainvis.wustl.edu/wiki/index.php/Caret:About
Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.
Proper citation: Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) Copy
A collection of images of the human nervous system focusing on disease and injury.
Proper citation: Human Nervous System Disease and Injury (RRID:SCR_006370) Copy
http://www.opencolleges.edu.au/informed/learning-strategies/
Interactive infographic of a brain exploring more than 100,000 chemical reactions, highlighted by areas and explanations of what that area is known to do.
Proper citation: Open Colleges Interactive Brain (RRID:SCR_001427) Copy
http://www.stat.cmu.edu/~fiasco/
Collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons.
Proper citation: Functional Image Processing software Computational Olio (RRID:SCR_001689) Copy
http://surfer.nmr.mgh.harvard.edu/
Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.
Proper citation: FreeSurfer (RRID:SCR_001847) Copy
http://www.brain-dynamics.net/
The Brain Dynamics Centre (BDC) is a network of centers and units. It achieves a unique exploration of the healthy brain and disorders of brain function. It translates these insights into new ways to tailor treatments to the individual. There approach is: "integrative neuroscience" - bringing together clinical observations, theory, and modern imaging technologies. And it's theoretical framework derives from linking physiology, psychology and evolution. Additionally, BDC also actively researches ADHD and conduct disorder, stress and trauma-related problems, depression and anxiety, anorexia nervosa, psychosis (including early onset) and conversion disorders. The research facilities DBC include assessment, rooms, two cognition-brain function laboratories, genotyping and an MRI Suite with 1.5 and 3T GE systems. BDC is the coordinating site for an international network - BRAINnet. It has over 180 members, and coordinates access to the first standardized database on the human brain for scientific purposes: Brain Resource International Database.
Proper citation: Brain Dynamics Centre (RRID:SCR_001685) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Duke Image Analysis Laboratory (DIAL) is committed to providing comprehensive imaging support in research studies and clinical trials to various agencies. The capabilities of the lab include protocol development, site training and certification, and image archival and analysis for a variety of modalities including magnetic resonance imaging, magnetic resonance spectroscopy, computed tomography and nuclear medicine. DIAL uses the latest technologies to analyze Magnetic Resonance Imaging (MRI) data sets of the brain. Currently the lab is engaged in measurement of the hippocampus, amygdala, caudate, ventricular system, and other brain regional volumes. Each of these techniques have undergone a rigorous validation process. The measurements of brain structures provide a useful means of non-invasively testing for changes in the brain of the patient. Changes over time in the brain can be detected, and evaluated with respect to the treatment that the patient is receiving. Magnetic Resonance Spectroscopy (MRS) allows DIAL to obtain an accurate profile of the chemical content of the brain. This sensitive technique can detect small changes in the metabolic state of the brain; changes that vary in response to administration of therapeutic agents. The ability to detect these subtle shifts in brain chemistry allows DIAL to identify changes in the brain with more sensitivity than allowed by image analysis. In this respect, NMR spectroscopy can provide early detection of changes in the brain, and serves to compliment the data obtained from image analysis. Additionally, DIAL also contains SQUID (Scalable Query Utility and Image Database). It is an image management system developed to facilitate image management in research and clinical trials: SQUID offers secure, redundant image storage and organizational functions for sorting and searching digital images for a variety of modalities including MRI, MRS, CAT Scan, X-Ray and Nuclear Medicine. SQUID can access images directly from DUMC scanners. Data can also be loaded via DICOM CDs, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Duke University Medical Center: Duke Image Analysis Laboratory (RRID:SCR_001716) Copy
http://www.gmu.edu/departments/krasnow/
The Krasnow Institute seeks to expand understanding of mind, brain, and intelligence by conducting research at the intersection of the separate fields of cognitive psychology, neurobiology, and the computer-driven study of artificial intelligence and complex adaptive systems. These separate disciplines increasingly overlap and promise progressively deeper insight into human thought processes. The Institute also examines how new insights from cognitive science research can be applied for human benefit in the areas of mental health, neurological disease, education, and computer design. It is this informed access to mind and brain that is the core of the mission of The Krasnow Institute. While their goals and tools are scientific, they also are fully cognizant of the applications of the results for the benefit of mankind, in areas like mental health, neurological diseases, and computer design. In asking the major questions they realized the necessity of being flexible, innovative, and trans-disciplinary. Therefore, they became dedicated to bringing together scholars from a wide variety of specialties and providing a milieu where they can be both productive and interactive. This institute will provide these researchers with the tools required to move ahead and create an environment of optimal scientific integrity coupling innovation with risk taking. The Krasnow institute is especially attuned to the deep insights from evolutionary biology, which is at the root of understanding all organismic functions including cognition; computer studies of complex systems, which present a revolution in our ability to deal with the world of interactive agents; and a long history of cognitive psychology, which provides a huge data base of human abilities and responses. It also continues to develop its long-term research program based on the contributions of George Mason University faculty holding joint appointments at Krasnow and other GMU academic departments. Additionally, the Krasnow Institute Department of Molecular Neuroscience, together with the College of Science (COS) and the College of Humanities and Social Sciences (CHSS), oversees the campus-wide Neuroscience Council in developing the Neuroscience PhD curriculum. Research groups in the Krasnow institute include: - Adaptive Systems Laboratory - Center for Neural Dynamics - Center for Social Complexity - Center for the Study of Neuroeconomics o Neuroeconomics Laboratory - Comparative Vertebrate Neurobiology Research Group - Center for Neuroinformatics, Neural Structures, and Neuroplasticity (CN3) o Computational and Experimental Neuroplasticity (CENlab) o Computational Neuroanatomy Group o Physiological and Behavioral Neuroscience in Juveniles (PBNJ) Lab - Receptor Complexes and Signaling Lab - Krasnow Investigations of Developmental Learning and Behavior (KIDLAB) - Neuro Imaging Core of the Krasnow Institute
Proper citation: George Mason University: Krasnow Institute for Advanced Study (RRID:SCR_001741) Copy
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