Tools   Select Another Resource Report Type

http://www.med.unc.edu/bric/ideagroup/free-softwares/abeat-a-toolbox-for-consistent-analysis-of-longitudinal-adult-brain-mri

A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

Proper citation: aBEAT (RRID:SCR_002238) Copy   

•   Source: SciCrunch Registry

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

Software package that performs several multivariate and mass univariate lesion symptom mapping analyses. Uses patient imaging lesion masks of brain insults and correlates them in multiple ways with patient behavioral and covariate data. Several permutation based SPMs are computed along with power, variance explained, and lesion coverage maps.

Proper citation: CLIMB Lesion Symptom Mapping Software (RRID:SCR_018298) Copy   

•   Source: SciCrunch Registry

http://spot.colorado.edu/~dubin/talks/agnosia.html

Compilation terms with definitions that describe altered states that are associated with brain injury (e.g., trauma, stroke, tumor) or with developmental deficits. Although the list deals with primarily CNS-associated disorders, in some cases the term does not distinguish between a CNS cause or a peripheral or neuromuscular cause. Terms that are primarily psychiatric diagnoses (e.g., schizophrenia) are not included. AGNOSIA is a general term for a loss of ability to recognize objects, people, sounds, shapes, or smells; that is, the inability to attach appropriate meaning to objective sense-data. It usually is used when the primary sense organ involved is not impaired. APHASIA is a general term relating to a loss of language ability. APRAXIA is a general term for disorders of practice. These conditions are usually caused by brain injury due to trauma, stroke and/or tumor. Many of these terms have two synonymous forms that differ in whether the word starts with a- or with dys- such as alexia and dyslexia. Here the a- form is usually defined and the other is noted as syn:, except when the dys- form is the more common usage. (If you cannot find a term in one of these forms, look for it in the other. All other synonyms are defined in both forms.) Sources: These definitions are paraphrased from definitions in a large number or print and online dictionaries. Thus this list is not meant to be considered my own, but rather is a compilation. Note: When a word appears in italics, that indicates it is defined elsewhere in this list.

Proper citation: AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders (RRID:SCR_005336) Copy   

•   Source: SciCrunch Registry

http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Rat_Brain_Atlas.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 27,2025. Compact 3rd edition of The Rat Brain Atlas of Paxinos & Watson published in 1997, it is the most widely used stereotaxic reference system for rat brain. The illustrations and nomenclature of the atlas have become standard tools used by almost all research neuroscientists who deal with anatomy, physiology, or function. It has been subsequently updated, with the 6th edition being the most recent. The 3rd edition is the most recent one available online for free. The program runs in Adobe Acrobat Reader.

Proper citation: Rat Brain Atlas of Paxinos and Watson (RRID:SCR_006369) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/Macaque

A reference atlas of standard macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual macaque monkeys and studies. We have used MRI volumes from a group of 25 normal adult macaque monkeys (18 Macaca fascicularis, 7 Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous macaque brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the MNI macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Macaque Atlas (RRID:SCR_005265) Copy   

•   Source: SciCrunch Registry

http://neurosynth.org

Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.

Proper citation: NeuroSynth (RRID:SCR_006798) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/

Center dedicated to understanding and treatment of neurological diseases by creating and using imaging methods to study human nervous system. Dedicated to research imaging of human brain. Brain structure is imaged using anatomical Magnetic Resonance Imaging (aMRI) while brain physiology is imaged using Positron Emission Tomography (PET), Magnetic Resonance Spectroscopy (MRS), functional MRI (fMRI) and magnetoencephalography (MEG). BIC maintains linkages with clinical, clinical research and basic research communities within Montreal Neurological Institute (MNI), McGill University and has collaborations across Quebec, Canada, USA and internationally.

Proper citation: McConnell Brain Imaging Center (RRID:SCR_008364) Copy   

•   Source: SciCrunch Registry

http://www.uab.edu/cnc

The overall mission of the Comprehensive Neuroscience Center (CNC) is to promote and support interdisciplinary neuroscience research, clinical care and education at UAB. Despite significant advances over the last 15 years in understanding many basic neurological processes, development of more effective treatments for neurological and psychiatric diseases have been identified as the largest and fastest growing unmet medical need in this country. The institutions that can most rapidly and creatively establish the necessary neuroscience initiatives to facilitate the translation of basic research discoveries into effective therapies will be positioned to lead neurological and psychiatric disease research into the future. The Center integrates a variety of disciplines, including neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, and biomedical engineering. Faculty from the Schools of Medicine, Optometry, Social and Behavioral Sciences, Dentistry, Engineering, Health Professions, and Public Health are affiliated with the Center. The need to address neuroscience research is great: one in three Americans are affected by nervous system diseases including brain and spinal cord injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, and autism. The burden of these diseases has an estimated economic cost of 500 billion per year in the United States. Center Research: The CNC serves as a vital center for neuroscience research at UAB and oversees six thematic programs of investigation: neurodevelopment and neurogenetics, neurodegeneration and experimental therapeutics, neuroregeneration and plasticity, behavioral and cognitive health, glial biology in medicine, and neuroimaging. The CNC helps coordinate the efforts of multiple neuroscience related centers at UAB, such as the Center for Glial Biology in Medicine, the Evelyn F. McKnight Brain Institute, the Civitan International Research Center, and the Alzheimers Disease Research Center. By interacting directly with these centers and establishing coalitions of centers and neuroscience subdisciplines, the CNC aids the UAB neuroscience community in meeting the challenges of modern neuroscience investigation. The CNC builds on other recent advances in neuroscience at UAB, including an 8.6 million grant from the National Institutes of Health to establish the Alabama Neuroscience Blueprint Core Center Facility awarded in September 2006. The Neuroscience Blueprint establishes research infrastructure on campus that is shared by investigators from institutions across Alabama and the Southeast. UAB has also added dynamic new leadership in the neuroscience fields including the following new chairs: Ray L. Watts, MD, Neurology (from Emory University); David Sweatt, PhD, Neurobiology (from Baylor College of Medicine); and James Meador-Woodruff, MD, Psychiatry (from the University of Michigan).

Proper citation: UAB Comprehensive Neuroscience Center (RRID:SCR_007195) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/Cyno

A reference atlas of cynomolgus macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual cynomolgus monkeys and studies. We have used MRI volumes from a group of 18 normal adult cynomulgus monkeys (Macaca fascicularis) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous cynomolgus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the cynomolgus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas (RRID:SCR_008793) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj2

An unbiased magnetic resonance imaging template brain volume for pediatric data from birth to 4.5y age range. These volumes were created using 317 scans from 108 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Templates are constructed for different age ranges. Each age range includes an average T1w, T2w, PDw maps normalized between 0 and 100. Also each age range includes a binary brain mask. Tools for using these atlases can be found in the Software section.

Proper citation: NIHPD Objective 2 atlases (birth - 4.5 years) (RRID:SCR_008795) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/Rhesus

A reference atlas of rhesus macaque monkey magnetic resonance images that offers a common stereotaxic reference frame. The atlas can be used to localize anatomical and functional information in an organized and reliable way for comparison across individual rhesus monkeys and studies. We have used MRI volumes from a group of 7 normal adult rhesus monkeys (Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous rhesus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the rhesus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Rhesus Macaque Atlas (RRID:SCR_008790) Copy   

•   Source: SciCrunch Registry

http://www.neurobiologie.fu-berlin.de/beebrain

Standard brain atlas of the honeybee presented as an interactive three-dimensional surface model with integrated neuron and neuronal tracts. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The Honeybee, Apis mellifera has been studied extensively with respect to its sensory and neural capacities in navigation, communication, visual and olfactory learning and memory processing. The goal is to integrate the entirety of information into a Virtual Atlas of the Honeybee Brain. This common spatial reference map will potentiate the representation of structural and functional data obtained in different experiments and from different individuals.

Proper citation: Virtual Atlas of the Honeybee Brain (RRID:SCR_007133) Copy   

•   Source: SciCrunch Registry

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

An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997).

Proper citation: Brainvox (RRID:SCR_009448) Copy   

•   Source: SciCrunch Registry

http://brain.io/

A startup research, development and innovation company based in The Grand Duchy of Luxembourg working on four major areas: Open Research, as Information Hub; Information Technology, as The Common Brain; Collective Awareness, as Manifesto; and Biophysics, as Human Extensibility. The Information Hub researches a methodology to conduct open research using a collaborative approach designed for multi-disciplinary interventions, multi-scope goal alignment, advanced analytics and a unified research experience for international cooperation. The Common Brain researches an open source intelligent architecture for future internet, one that is deeply sustainable over a highly distributed hybrid network, self-governed, heterogenous, and logical. Manifesto researches a methodology for a collaborative approach for policy making, open standardization, accreditation, verification and compliance. Human Extensibility researches the establishment of the scientific ground for a field of science concerned with the study of the physics and physiology of the human being, to provide techniques and genetic algorithms for human extensibility.

Proper citation: Brain.io (RRID:SCR_014527) Copy   

•   Source: SciCrunch Registry

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

A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.

Proper citation: BROCCOLI (RRID:SCR_014093) Copy   

•   Source: SciCrunch Registry

http://www.rad.upenn.edu/sbia/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher.

Proper citation: SBIA (RRID:SCR_013628) Copy   

•   Source: SciCrunch Registry

http://www.chimpanzeebrain.org/

Collection and distribution of chimpanzee neuroimaging data and postmortem brain tissue. Portal to access chimpanzee brain atlas tools, data repository, bibliography of publications, educational information, and links to other chimpanzee brain resources and datasets on the Internet. Serves as repository for in vivo structural MRI scans of chimpanzee brains, in vivo and postmortem diffusion tensor images (DTI), as well as postmortem fixed and frozen brain specimens.

Proper citation: National Chimpanzee Brain Resource (RRID:SCR_019183) Copy   

•   Source: SciCrunch Registry

https://github.com/afids

Open framework for evaluating correspondence between brain images and teaching neuroanatomy.

Proper citation: AFIDs (RRID:SCR_016623) Copy   

•   Source: SciCrunch Registry

http://portal.brain-map.org/

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

•   Source: SciCrunch Registry

https://kinarm.com/solutions/kinarm-end-point-lab/

Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force.

Proper citation: Kinarm: End-Point Lab (RRID:SCR_017060) Copy   

•   Source: SciCrunch Registry