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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520032/
Algorithm for computational imaging of MRI data that detects and quantifies ischemic core–penumbra using only a single MRI modality (T2- or diffusion-weighted imaging, T2WI/DWI). It can be used with 3D data on lesions and normal-appearing brain matter (NABM) volumes.
Proper citation: Hierarchical Region Splitting (RRID:SCR_016398) Copy
https://www.nitrc.org/projects/mrtool
Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12.
Proper citation: MRTool (RRID:SCR_015956) Copy
http://www.thebrainproject.org/
The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been made utilizing the principles of open source a research method that promotes free and open access to the design and production of goods and knowledge. Its use was made well-known through the creation of the Linux computer operating system, in which professionals share knowledge to make corrections and fix problems. Open source is commonly used by millions of people today through the Wikipedia online free encyclopedia, a collection of public entries on established subjects that allows anyone to make additions or corrections. The National Institute of Mental Health launched The Human Brain Project in 1993 to develop and support the new science of neuro-informatics. From this initiative, it became obvious what needed to be done. That's why we created the Sarah Jane Brain Virtual Center of Excellence an ecosystem for professionals and families dealing with PABI around the world and a vehicle to help implement the PABI Plan by establishing a model system for PABI.
Proper citation: Sarah Jane Brain Project (RRID:SCR_000620) Copy
http://isc.temple.edu/neuroanatomy/lab/atlas/S5/
Sectional atlas featuring sections of the spinal cord and brain for a neuroanatomy course offered by Temple University. Labels may be turned on and off.
Proper citation: Sectional Atlas of Human Brain and Spinal Cord (RRID:SCR_000799) Copy
https://lcn.salk.edu/WSMain.html
The Salk Institute's Laboratory for Cognitive Neuroscience (LCN) is dedicated to the study of the neural and genetic underpinnings of language and cognition. The LCN organizes its resources into two research foci: Linking Gene, Brain, and Cognition, and Language, Modality and the Brain. Linking Gene, Brain, and Cognition: Behavioral Neurogenetics: - This research is designed to increase the understanding of genetically based disorders, to investigate the consequences of genetic alterations on the development of the brain, and to explore the resulting alteration of cognitive capabilities. Language, Modality, and the Brain: - The focus of this research is to obtain a greater understanding of how language and cognition are represented in the brain. Sponsors: This resource is supported by LCN.
Proper citation: Salk Institute for Medical Research: Laboratory for Cognitive Neuroscience (RRID:SCR_001851) Copy
Computational neuroscience center that observes and models how functional activities in multiple brain areas interact dynamically to support human cognition, creativity and social interaction. Center research involves development computational methods and software, experimental methods and equipment, collection and analysis of human cognitive experiments, and collaborations to analyze data collected by other groups in such experiments. The Center has a 72-channel EEG recording system customized for use in the fMRI environment, and a very-high density Biosemi Active Two active-electrode EEG system, rapidly configurable either as a 256-channel system for a single subject or as two 136-channel systems for recording from two subjects simultaneously. In addition, UCSD now has a 306-channel MEG plus 128-channel EEG system (Neuromag/Elektra). Projects in the Center include studies of human cognitive processes including attention and memory, role of the anterior/posterior cingulate, time perception and emotional expression. Data acquisition includes high-density EEG, concurrent EEG and fMRI recording and analysis, and face video processing. Current analysis approaches include independent component and time-frequency analysis.
Proper citation: Swartz Center for Computational Neuroscience (RRID:SCR_001933) Copy
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
An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI).
Proper citation: HUPO Brain Proteome Project (RRID:SCR_007302) Copy
https://github.com/BlueBrain/BluePyOpt
An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.
Proper citation: BluePyOpt (RRID:SCR_014753) Copy
Research facility for research on neurological and psychiatric disorders on the learning brain and the aging brain. The Centre utilizes a multidisciplinary approach to explore the causes and potential treatments of disorders like Alzheimer's disease, mental health and addiction, stroke and neurotrauma. The Centre focuses on translating research into patient care and therapies.
Proper citation: Djavad Mowafaghian Centre for Brain Health (RRID:SCR_013149) Copy
http://www.icn.ucl.ac.uk/motorcontrol/
Using robotic devices to investigate human motor behavior, this group develops computational models to understand the underlying control and learning processes. By simulating novel objects or dynamic environments they study how the brain recalibrates well-learned motor skills or acquires new ones. These insights are used to design fMRI studies to investigate how these processes map onto the brain. They have developed a number of novel techniques of how to study motor control in the MRI environment, and how to analyze MRI data of the human cerebellum. They also study patients with stroke or neurological disease to further determine how the brain manages to control the body.
Proper citation: UCL Motor Control Group (RRID:SCR_005271) Copy
The FMRIB Centre is a multi-disciplinary neuroimaging research facility, which focuses on the use of Magnetic Resonance Imaging (MRI) for neuroscience research, along with related technologies such as Transcranial Magnetic Stimulation, transcranial Direct Cortical Stimulation and EEG. FMRIB is composed of research groups in all aspects of brain imaging research, including physics, analysis, basic science and clinical neuroscience. We were recently awarded 8 million pounds by the MRC, EPSRC, Wolfson Foundation and University of Oxford to purchase and install new 7T and 3T leading-edge MRI systems to enable us to image brain structure and function at even higher resolution than currently possible.
Proper citation: Oxford Centre for Functional MRI of the Brain (RRID:SCR_005283) Copy
Leading treatment, research and teaching center for complex neurological conditions based at the University Hospital and the UC College of Medicine. Its physicians and researchers have created national models for evidence-based treatment and research of complex conditions, including ischemic and hemorrhagic stroke, brain aneurysms, brain and spinal cord trauma, brain tumors, Parkinson's disease, epilepsy and seizure disorders, multiple sclerosis, trigeminal neuralgia, Alzheimer's disease and memory disorders, mood disorders, and neuromuscular disorders. UCNI includes a team of more than 100 experts from 15 specialties who collaborate across disciplines to provide the most comprehensive diagnoses and treatments possible.
Proper citation: University of Cincinnati Neuroscience Institute (RRID:SCR_005345) Copy
http://www.rad.upenn.edu/sbia/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. Software package used to simulate brain images with local growth / atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions.
Proper citation: Atrophy Simulation Package (RRID:SCR_006046) Copy
https://www.braintest.org/brain_test/BrainTest
A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help.
Proper citation: Brain Test (RRID:SCR_006212) Copy
https://github.com/bheAI/MonkeyCBP_CLI
Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.
Proper citation: MonkeyCBP (RRID:SCR_017640) Copy
https://github.com/markmikkelsen/Gannet
Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.
Proper citation: Gannet (RRID:SCR_016049) Copy
http://www.humanconnectomeproject.org/
A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.
Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy
A web portal that aggregates information and educational materials about the brain and brain diseases. Resources such as videos, key brain concepts, and hands-on activities may be used and shared with the public.
Proper citation: brainfacts.org (RRID:SCR_003514) Copy
http://www.pediatricmri.nih.gov/
Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2.
Proper citation: NIH MRI Study of Normal Brain Development (RRID:SCR_003394) Copy
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