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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   

•   Source: SciCrunch Registry

http://dally.nimh.nih.gov/index.html

A program developed by the NIMH Laboratory of Neuropsychology for data acquisition and experimental control of neurophysiological experiments. The purpose of this website is to make it easier to access new versions of NIMH CORTEX and its supporting documents. Ultimately, it is also hoped that these pages will make it easier for users to report bugs, request enhancements, and obtain help. Download the latest version and unzip it into a new sub-directory. Then read the on-line documentation. For the new user, the User''s Manuals are invaluable in specifying system requirements and giving an overview of the features and necessary hardware. The Function reference goes into more detail about how to write experiments using NIMH CORTEX. The Demos reference is a good place for new and experienced users to start to get an idea of what NIMH CORTEX can do these days.

Proper citation: NIMH CORTEX (RRID:SCR_006837) Copy   

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https://trialweb.dcri.duke.edu/tads/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression.

Proper citation: TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) Copy   

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https://resource.loni.usc.edu/resources/atlases/

Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.

Proper citation: International Consortium for Brain Mapping (RRID:SCR_000445) Copy   

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http://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

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http://fantom.gsc.riken.jp/

International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.

Proper citation: Functional Annotation of the Mammalian Genome (RRID:SCR_000788) Copy   

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http://www.sfn.org/SiteObjects/published/0000BDF20016F63800FD712C30FA42DD/1304F8BE908CE526359306C138737F9F/file/NRF%20Contacts.pdf

This resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units.

Proper citation: NRF Contacts (RRID:SCR_001473) Copy   

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

Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

Proper citation: VoxBo (RRID:SCR_002166) Copy   

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http://gara.bio.uci.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.

Proper citation: Glomerular Activity Response Archive (RRID:SCR_002089) Copy   

•   Source: SciCrunch Registry

http://www.brainarchitecture.org/mouse-home

An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset.

Proper citation: Mouse Brain Architecture Project (RRID:SCR_004683) Copy   

•   Source: SciCrunch Registry

https://bams1.org/ontology/viewer.php

Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts.

Proper citation: BAMS Neuroanatomical Ontology (RRID:SCR_004616) Copy   

•   Source: SciCrunch Registry

http://openneuro.org

Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.

Proper citation: OpenNeuro (RRID:SCR_005031) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/about/advisory-boards-and-groups/namhc/reports/mri-research-safety-ethics.pdf

NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities.

Proper citation: MRI Research Safety and Ethics (RRID:SCR_005642) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/educational-resources/brain-basics/brain-basics.shtml

Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression.

Proper citation: Brain Basics (RRID:SCR_005606) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/research-funding/training/index.shtml

A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity.

Proper citation: NIMH Resources for Research Training and Career Development (RRID:SCR_005624) Copy   

•   Source: SciCrunch Registry

http://headit.ucsd.edu

Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al.

Proper citation: HeadIT (RRID:SCR_005657) Copy   

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https://kimlab.io/brain-map/epDevAtlas/

Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology.

Proper citation: Early Postnatal Developmental Mouse Brain Atlas (RRID:SCR_024725) Copy   

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http://www.agre.org/index.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A private repository of clinical and genetic information on families with autism. Genetic and clinical data are obtained from families that have more than one family member diagnosed with an Autism Spectrum Disorder. The biological samples, along with the accompanying clinical data, are made available to AGRE-approved researchers worldwide. As they become available, additional family pedigrees will be posted in the online catalog. Cell lines have been established for the majority of families in this collection and serum/plasma is available on a subset of the subjects until stocks are depleted. The diagnosis of autism has been made using the standard Autism Diagnostic Interview-Revised (ADI-R) algorithm and the Autism Diagnostic Observation Scale (ADOS-G). Detailed birth and medical histories (including basic dysmorphology assessments) on children as well as family and medical information for parents and unaffected siblings, are available for nearly all families. DNA, cell lines, serum, plasma and clinical information are made available to AGRE-approved researchers for analysis.

Proper citation: Autism Genetic Resource Exchange (RRID:SCR_004403) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/pro/nyu.html

Datasets including a collection of scans from 49 psychiatrically evaluated neurotypical adults, ranging in age from 6 to 55 years old, with age, gender and intelligence quotient (IQ) information provided. Future releases will include more comprehensive phenotypic information, and child and adolescent datasets, as well as individuals from clinical populations. The following data are released for every participant: * At least one 6-minute resting state fMRI scan (R-fMRI) * * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * Two 64-direction diffusion tensor imaging scans * Demographic information (age, gender) and IQ-measures (Verbal, Performance, and Composite; Weschler Abbreviated Scale of Intelligence - WASI) * Most participants have 2 R-fMRI scans, collected less than 1 hour apart in the same scanning session. Rest_1 is always collected first.

Proper citation: NYU Institute for Pediatric Neuroscience Sample (RRID:SCR_010458) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/abide/

Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.

Proper citation: ABIDE (RRID:SCR_003612) Copy   

•   Source: SciCrunch Registry