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http://pingstudy.ucsd.edu/

A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.

Proper citation: Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) Copy   

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http://www.bumc.bu.edu/busm-pathology/pathology-core-services/biospecimen-archive-research-core-barc/

Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org

Proper citation: Boston University Biospecimen Archive Research Core (RRID:SCR_005363) Copy   

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http://www.youtube.com/user/WholeBrainCatalog?feature=autoshare

Videos uploaded to YouTube by the Whole Brain Catalog.

Proper citation: WholeBrainCatalog's Channel - YouTube (RRID:SCR_005436) Copy   

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http://cmrm.med.jhmi.edu/cmrm/atlas/human_data/file/JHUtemplate_newuser.html

DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.

Proper citation: DTI White Matter Atlas (RRID:SCR_005279) Copy   

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http://med.brown.edu/neurology/brainbank/index.html

A tissue resource center which facilitates research into the relationship between Alzheimer's disease and other brain disorders such as strokes and mental illnesses. Most donations have been obtained from Alzheimer's patients. Normal controls are available, many of which are from subjects with close relatives with Alzheimer's. The Brown BTRC also supports a collection of brain tumor cases that were harvested from patients who underwent surgery and who were enrolled in a clinical trial for the development of new treatments for brain cancer.

Proper citation: Brown Brain Tissue Resource Center (RRID:SCR_005392) Copy   

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http://neurosphere.wordpress.com/

This blog belongs to me, Dave J Hayes PhD, a Neuroscientist at the University of Ottawa''s Institute of Mental Health Research. My research focuses on the neuroscience of motivation and emotion particularly regarding how brains and people respond to aversive and rewarding things in their environment. A neurosphere is a free-floating group of neural stem cells which can multiply, outside of their natural environment, and retain the ability to differentiate into functional brain cells. I don''t work on neurospheres. However, i like the metaphor of a group of people coming together, outside of their natural environment, through their interest in all things neuro which, incidentally, is everything. The sphere of human thought.

Proper citation: neurosphere (RRID:SCR_005478) Copy   

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http://www.youtube.com/user/sfnvideo

The Society for Neuroscience (SfN) is a nonprofit membership organization of scientists and physicians who study the brain and nervous system. SFNVideo - YouTube are videos uploaded to YouTube by the Society for Neuroscience (SfN). Since inception in 1969, the Society has grown from 500 members to more than 41,000. Today, SfN is the world''s largest organization of scientists and physicians devoted to advancing understanding of the brain and nervous system.

Proper citation: sfnvideo - YouTube (RRID:SCR_005463) Copy   

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https://www.youtube.com/user/iniusc

Videos uploaded to YouTube by the Laboratory of Neuro Imaging (LONI). The Laboratory of Neuro Imaging at UCLA strives to improve our understanding of the brain in health and disease. LONI is a leader in the development of advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function.

Proper citation: Laboratory of Neuro Imaging - YouTube (RRID:SCR_005462) Copy   

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http://www.dartmouth.edu/~rswenson/Atlas/

On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV)

Proper citation: Atlas of the Brain (RRID:SCR_005967) Copy   

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http://neurodojo.blogspot.it/

A blog by Zen Faulkes, an invertebrate neuroethologist at The University of Texas-Pan American.

Proper citation: NeuroDojo (RRID:SCR_006237) Copy   

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http://neurocritic.blogspot.com/

The Neurocritic is a blog deconstructing the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology. Born in West Virginia in 1980, The Neurocritic embarked upon a roadtrip across America at the age of thirteen with his mother. She abandoned him when they reached San Francisco and The Neurocritic descended into a spiral of drug abuse and prostitution. At fifteen, The Neurocritic''s psychiatrist encouraged him to start writing as a form of therapy.

Proper citation: Neurocritic (RRID:SCR_006528) Copy   

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http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

Proper citation: Adult Wistar Rat Atlas (RRID:SCR_006288) Copy   

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

Database of 141 studies which have investigated brain structure (using MRI and CT scans) in patients with bipolar disorder compared to a control group. Ninety-eight studies and 47 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website.

Proper citation: Bipolar Disorder Neuroimaging Database (RRID:SCR_007025) Copy   

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http://cocomac.g-node.org/main/index.php?

Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute.

Proper citation: CoCoMac (RRID:SCR_007277) Copy   

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http://www.oasis-brains.org/

Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.

Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) Copy   

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http://brainhack.org/

Forum for collaborative projects in the field of brain science. Everyone is invited to submit projects, either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative, open way.

Proper citation: brainhack.org (RRID:SCR_000195) Copy   

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http://www.cnbc.cmu.edu/

CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.

Proper citation: Center for the Neural Basis of Cognition (RRID:SCR_002301) Copy   

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http://rfmri.org/DPARSF

A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely.

Proper citation: DPARSF (RRID:SCR_002372) Copy   

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http://mindboggle.info

Mindboggle (http://mindboggle.info) is open source software for analyzing the shapes of brain structures from human MRI data. The following publication in PLoS Computational Biology documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350

Proper citation: Mindboggle (RRID:SCR_002438) Copy   

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http://aimlab.cs.uoregon.edu/NEMO/web/

THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Neural ElectroMagnetic Ontologies (NEMO) Project (RRID:SCR_002001) Copy   

•   Source: SciCrunch Registry