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https://sites.google.com/site/functionalconnectivitytoolbox/

MATLAB toolbox for performing functional connectivity analyses includes many of the most commonly-used approaches researchers have utilized to date for the identification of condition-dependent functional interactions between fMRI time-series obtained from two or more brain regions. The approaches are either bivariate or multivariate methods defined in time or frequency domains that emphasize distinct features of relationships among the time-series.

Proper citation: Functional Connectivity Toolbox (RRID:SCR_006394) Copy   

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http://www.medschool.lsuhsc.edu/epilepsy_center/

The LSU Epilepsy Center of Excellence is dedicated to providing state-of-the-art, comprehensive epilepsy treatment, enhancing access to epilepsy education for patients and physicians, and promoting multidisciplinary epilepsy research in pharmacology, neuroelectrophysiology, neuroimaging, neurosurgery, neuropsychology, biomedical engineering and public health. The center''s team of professionals offers diagnostic and presurgical monitoring, the strategic use of antiepileptic medications, specialized epilepsy neuroimaging, vagus nerve stimulator implantation, ketogenic diet management, neuropsychological testing, psychiatric support and epilepsy surgery for adults and children. The Center also hosts several clinical research trials each year for investigational medications and devices. The following are the treatment methods currently available at this center: - Epilepsy Brain Implants - Responsive Neurostimulator (RNS) - Medications - Medication blood level monitoring - Vagus Nerve Stimulators (VNS) - Epilepsy Surgery - Ketogenic Diet - Psychiatric Services - Radiosurgery Epilepsy Center Sections: *Electrophysiology *Neuroimaging *Neuropsychology *Neuroscience *Neurosurgery *Pharmacology *Psychiatry *Research

Proper citation: Louisiana State University School of Medicine, Health Sciences Center: Epilepsy Center (RRID:SCR_006519) Copy   

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http://www.mitre.org/news/digest/archives/2002/neuroinformatics.html

This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.

Proper citation: MITRE Neuroinformatics (RRID:SCR_006508) Copy   

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http://www.neuroinf.jp/

The Japan Node of the INCF coordinates neuroinformatics activities within Japan and represents Japanese efforts in INCF. This site provides information about Japanese neuroinformatics platforms (NI Platforms) and the techniques and tools available from the International Neuroinformatics Coordinating Facility (INCF). The Neuroinformatics Japan Center (NIJC) will also supply techniques and tools developed at RIKEN BSI and at other research groups in Japan. INCF expects each national node to: 1. Actively formulate and implement the INCF Work Programs, 2. Coordinate and facilitate local neuroinformatics research activities at the national level, 3. Encourage neuroinformatics data sharing that conforms with INCF standards, and 4. Promote neuroinformatics development that supports the goals of INCF. The Neuroinformatics Japan Center (NIJC) represents the Japan Node. Together with the Japan Node Committee and the Platform Subcommittees, we promote domestic activities of neuroinformatics. Platform Subcommittee members collaborate to develop databases that are available for use on the website. Standing at the intersection of neuroscience and information science, the field of neuroinformatics develops the tools to house, share and analyze neuroscientific data, and to create computational models of brain. NIJC supports researchers developing and maintaining neuroscience databases, provides a portal for these databases and Neuroinformatics, and is designing the infrastructure for Neuroinformatics. It is also developing database technologies, and facilitates cooperation and distribution of the information stored in those databases. The activities of the Japan Node * Shaping domestic neuroinformatics research and directions (Japan Node Committee) * Advising on Intellectual Property Rights and protecting experimental subjects (Japan Node Committee) * Developing and publishing brain science databases (Platform Subcommittee) * Coordinating database management (Platform Subcommittee) * Disseminating neuroinformatics information via the web portal * Developing the infrastructure for brain science information and neuroinformatics * Supporting the development and diffusion of neuroinformatics technology

Proper citation: INCF Japan Node (RRID:SCR_006569) Copy   

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http://learn.genetics.utah.edu/content/addiction/drugs/mouse.html

Mouse Party is an interactive website that teaches how various drugs disrupt the synapse by taking a look inside the brains of mice on drugs! Every drug of abuse has its own unique molecular mechanism. Where applicable, this presentation primarily depicts how drugs interact with dopamine neurotransmitters because this website focuses on the brain''s reward pathway. Mouse Party is designed to provide a small glimpse into the chemical interactions at the synaptic level that cause the drug user to feel ''high''. The simplified mechanisms of drug action presented here are just a small part of the story. When drugs enter the body they elicit very complex effects in many different regions of the brain. Often they interact with many different types of neurotransmitters and may bind with a variety of receptor types in a variety of different locations. For example, THC in marijuana can bind with cannabinoid receptors located on the presynaptic and/or postsynaptic cell in a synapse.

Proper citation: Mouse Party (RRID:SCR_006438) Copy   

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http://users.loni.ucla.edu/~shattuck/brainsuite/

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

Proper citation: BrainSuite (RRID:SCR_006623) Copy   

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http://www.biausa.org/

The country''s oldest and largest nationwide brain injury advocacy organization. We are dedicated to increasing access to quality health care and raising awareness and understanding of brain injury through advocacy, education and research. With a nationwide network of more than 40 chartered state affiliates and hundreds of local chapters and support groups, we provide help, hope and healing for individuals who live with brain injury, their families and the professionals who serve them. Brain injury is not an event or an outcome. It is the start of a misdiagnosed, misunderstood, under-funded neurological disease. Individuals who sustain brain injuries must have timely access to expert trauma care, specialized rehabilitation, lifelong disease management and individualized services and supports in order to live healthy, independent and satisfying lives.

Proper citation: Brain Injury Association of America (RRID:SCR_006639) Copy   

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http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

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http://www.brainvoyager.com

Brain Innovation B.V. is developing scientific software in the field of human and animal brain imaging, neural network simulation and computer-based experimental control. Our current major product, BrainVoyager QX, is a commercially available cross-platform neuroimaging tool, which is used in hundreds of labs across the planet. Turbo-BrainVoyager is an easy to use program for real-time data analysis, which allows to observe a subject''s or patient''s brain activity during an ongoing functional MRI scanning session. TMS Neuronavigator provides the hard- and software to navigate a TMS coil to desired anatomical or functionally defined brain regions. We also provide free software products. BrainVoyager Brain Tutor allows to learn about brain areas by clicking on rotatable 3D brain models. StimulDX is a powerful stimulation software based on Microsofts DirectX API, which we will make available for free download in the near future.

Proper citation: Brain Innovation: Home of the BrainVoyager Product Family (RRID:SCR_006660) Copy   

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http://www.abta.org/

Founded in 1973, the American Brain Tumor Association (ABTA) was the first national nonprofit organization dedicated solely to brain tumors. For nearly 40 years, the Chicago-based ABTA has provided critical funding to researchers working toward breakthroughs in brain tumor diagnosis, treatment and care, and is the only national organization providing comprehensive resources and serving the complex supportive care needs of brain tumor patients and caregivers from diagnosis through treatment and beyond.

Proper citation: American Brain Tumor Association (RRID:SCR_006649) Copy   

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http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

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http://www.brainvoyager.com/products/braintutor.html

A free award-winning educational program that teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex. The program runs on Windows XP, Vista and Windows 7.

Proper citation: BrainVoyager Brain Tutor (RRID:SCR_006737) Copy   

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http://neurovault.org/

Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies.

Proper citation: NeuroVault (RRID:SCR_003806) Copy   

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http://www.mrc-cbu.cam.ac.uk/

Unit studying human cognition and the brain with about 90 researchers and postgraduate students investigating topics such as attention, emotion, language and memory. They are developing new treatments for depression, improving hearing through cochlear implants, and helping children to overcome memory problems. With a large collection of scientists engaged in both basic and translational research on the mind and brain, the Unit provides an exceptional training and academic environment that benefits postgraduate students and researchers at all levels. A significant part of their research makes use of brain imaging and they have excellent on-site facilities for magnetic resonance imaging (MRI) magnetoencephalography (MEG) and electroencephalography (EEG). They also have clinical facilities at Addenbrooke's Hospital. The Unit has close links both with the hospital and with Cambridge University.

Proper citation: MRC Cognition and Brain Sciences Unit (RRID:SCR_003818) Copy   

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http://rfmri.org/

A network for supporting resting-state fMRI (R-fMRI) related studies. It connects R-fMRI researchers (as nodes) by their sharings (as edges). Through the network, ideas, comments, resources, tools, experiences, and data can be shared. Researchers (nodes) with basic neuroscience, methodological, or clinical backgrounds can connect with each other in the network. It also contains a preprint server that allows neuroscientists to share their preprints, comment on each others research and get back valuable information about their experiments from their colleagues. This is based on the arXiv model. Ultimately, the network aims to enhance collaborations among researchers, especially to translate knowledge of basic neuroscience and methodology to clinical applications (bench to bedside).

Proper citation: RFMRI.ORG (RRID:SCR_004042) Copy   

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http://cibsr.stanford.edu/

The Center for Interdisciplinary Brain Sciences Research (CIBSR) at the Stanford University School of Medicine is dedicated to research that will improve the lives and well-being of individuals with disorders of the brain and improve knowledge of healthy brain and behavioral development. CIBSR research staff are dedicated to identifying biological and environmental risk factors, understanding disease pathophysiology and developmental outcomes, and developing new treatments for neurodevelopmental, neurogenetic and neuropsychiatric disorders of childhood onset. Our research studies are truly multi/interdisciplinary as they bring together experts from the fields of psychiatry, neurology, psychology, computer science, biostatistics and genetics to explore and seek answers for complex questions related to brain-behavior relationships. Active research at CIBSR includes: * Mutlimodal imaging of the brain utilizing anatomical and functional magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS). * Behavioral, cognitive, and physiological assessment to address questions concerning the influence of biological and environmental factors on outcome. * The development of new biological and cognitive-behavioral treatments. * Development of brain image analysis methods and software.

Proper citation: Stanford University, Center for Interdisciplinary Brain Sciences Research (RRID:SCR_004134) Copy   

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http://www.caneucre.org

Cre expressing mice under the control of promoters with a design focus on the brain. Each promoter is derived from human sequence, but the resulting expression is assessed in the mouse for the activation of a LacZ reporter gene by the Cre activity. Promoters tested as large MaxiPromoters (BACs inserted into the mouse genome) and MiniPromoters (plasmid-based sequences inserted either into the mouse genome or introduced within AAV viruses). The Cre-related project continues from the Pleiades Promoter Project. Here is the list of genes for which icre/ERT2 mice are currently in development: AGTR1, CARTPT, CLDN5, CLVS2, CRH, GABRA6, HTR1A, HTR1B, KCNA4, KDM5C, MKI67, NEUROD6, NKX6-1, NOV, NPY2R, NR2E1, OLIG2, POU4F2, SLITRK6, SOX1, SOX3, SOX9,, SPRY1, VSX2

Proper citation: CanEuCre (RRID:SCR_004159) Copy   

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https://www.uab.edu/medicine/alzheimers/

The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study.

Proper citation: UAB Alzheimer's Disease Center (RRID:SCR_004305) Copy   

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http://www.brainnet-europe.org/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Consortium of 19 brain banks across Europe with an aim to harmonize neuropathological diagnostic criteria and develop gold standards for quality, safety and ethics standards for brain banking. BrainNet Europe also contributes to research on rare diseases, such as: Pick''s disease or other rare forms of dementia, as well as to questions after the events in the aging brain. Anyone can be a donor - irrespective of disease of the central nervous system or not, because for research purposes, one does not only need tissue samples from ill donors, but also from healthy ones for comparison.

Proper citation: BrainNet Europe (RRID:SCR_004461) Copy   

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http://www.epilepsy.ie/index.cfm/spKey/research.html

Epilepsy Research Ireland is a non-profit organization (Charity CHY17527), run by a group of volunteers, who are dedicated to find cure for epilepsy by raising awareness and money for research. We can say cure now with much more confidence than we could even 10 years ago because recent advances in genetics, brain imaging and drug therapy, all hold out the promise of that holy grail the cure. We can also say with confidence that you can be part of that push by participating in this new foundation since we have collaborations with doctors and scientists all over Europe, the US and Australia, all of whom share the same goal. Epilepsy research, conducted by Epilepsy Research Ireland, is essential and will deliver benefits across the board. Research planned and already underway by Epilepsy Research Ireland will help develop and improve clinical skills; it will provide a knowledge base to develop new ways to manage and treat epilepsy; it will help in the evaluation of new medical advances. Ultimately we can improve the quality of care and provide greater understanding, better and more accurate diagnosis and more tailored treatments. Ireland is uniquely well-positioned, given its relatively homogenous population to make the goal, of making real discoveries in epilepsy research that will directly improve the lives of people with epilepsy, a realistic one.

Proper citation: Epilepsy Research Ireland (RRID:SCR_004448) Copy   

•   Source: SciCrunch Registry