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http://hermes.ctb.upm.es/

A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

Proper citation: HERMES (RRID:SCR_009584) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information.

Proper citation: ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) Copy   

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http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1

An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask.

Proper citation: NIHPD Objective 1 atlases (4.5 - 18.5y) (RRID:SCR_008794) Copy   

•   Source: SciCrunch Registry

http://rfmri.org/dpabi

Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI).

Proper citation: DPABI (RRID:SCR_010501) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Proper citation: TRACULA (RRID:SCR_013152) Copy   

•   Source: SciCrunch Registry

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

Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases.

Proper citation: 7T Structural MRI scans ATAG (RRID:SCR_014084) Copy   

•   Source: SciCrunch Registry

https://singlecell.broadinstitute.org/single_cell

Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.

Proper citation: Single Cell Portal (RRID:SCR_014816) Copy   

•   Source: SciCrunch Registry

https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405

Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.

Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy   

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https://www.synapse.org/#!Synapse:syn4921369/wiki/235539

Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.

Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) 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/pro/VirginiaTech.html

Dataset including a T1 weighted anatomical image as well as two 10-minute resting state scans acquired during the same session from 25 psychiatrically screened healthy adults (community sample) ranging in age from 18 to 65 years old, with age, sex, education level, and ethnicity provided. Some subjects also returned several weeks after the first scan for a second scanning session. The number of days between scan sessions, for subjects that had two sessions, is indicated in the demographics spreadsheet. The study scanning protocol included: # 13 sec localizer # 4 minute 38 second T1 weighted anatomical # Subject given instructions for resting state scan #1 # 10 minute 4 second resting state scan #1 # Subject given instructions for resting state scan #2 # 10 minute 4 second resting state scan #2 Scanning was performed on one of three different 3T Siemens TIM TRIOs at the Human Neuroimaging Lab at Baylor College of Medicine in Houston, Texas. All scans were acquired using the standard Siemen''s TIM 12-channel head matrix. The resting state scans were acquired with a custom sequence that is a slight modification to the standard Siemen''s EPI sequence that supports real-time fMRI. Images were acquired slightly oblique to minimize dephasing in the orbito-frontal cortex. Detailed scanning parameters are included in separate .pdf files.

Proper citation: Virginia Tech Carilion Research Institute Sample (RRID:SCR_010459) Copy   

•   Source: SciCrunch Registry

https://molbio.princeton.edu/core-facilities/confocal-microscopy

Core provides researchers with ability to visualize samples, from monolayers and small organisms, such as developing fly and fish embryos, to very thick sections from brain and other organ tissues by using instruments including laser point (LSCM) and field scanning confocal (CSU), Total Internal Reflectance Fluorescence (TIRF), Multi Photon (MP), and Widefield (WF). Services in imaging in mammalian cells, yeast cells, Drosophila and Zebrafish embryos and ovaries, bacteria, sections of brain and other tissues, in both fixed and live specimens, Quantitative imaging methods such as FRAP, FLIP, and FRET, software packages for image processing, analysis, and 3D image reconstruction.

Proper citation: Princeton University Confocal Microscopy Core Facility (RRID:SCR_017812) Copy   

•   Source: SciCrunch Registry

http://autopatcher.org/

Software tool for neuronal recording in intact brain.

Proper citation: Autopatcher (RRID:SCR_017464) Copy   

•   Source: SciCrunch Registry

http://blog.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog.

Proper citation: Whole Brain Catalog Blog (RRID:SCR_000582) Copy   

•   Source: SciCrunch Registry

https://www.upf.edu/web/ntsa/downloads/-/asset_publisher/xvT6E4pczrBw/content/2001-indications-of-nonlinear-deterministic-and-finite-dimensional-structures-in-time-series-of-brain-electrical-activity-dependence-on-recording-regi?p_r_p_assetEntryId=229569389&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_xvT6E4pczrBw_type=content&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_xvT6E4pczrBw_urlTitle=2001-indications-of-nonlinear-deterministic-and-finite-dimensional-structures-in-time-series-of-brain-electrical-activity-dependence-on-recording-regi&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_xvT6E4pczrBw_redirect=https%3A%2F%2Fwww.upf.edu%3A443%2Fweb%2Fntsa%2Fdownloads%3Fp_p_id%3Dcom_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_xvT6E4pczrBw%26p_p_lifecycle%3D0%26p_p_state%3Dnormal%26p_p_mode%3Dview%26p_r_p_assetEntryId%3D229569389%26_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_xvT6E4pczrBw_cur%3D0%26p_r_p_resetCur%3Dfalse#229569389

Five data sets containing quasi-stationary, artifact-free EEG signals both in normal subjects and epileptic patients were put in the web by Ralph Andrzejak from the Epilepsy center in Bonn, Germany. Each data set contains 100 single channel EEG segments of 23.6 sec duration.

Proper citation: EEG time series Data Sets (RRID:SCR_001579) Copy   

•   Source: SciCrunch Registry

http://www.fmri.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease secondary to stroke or neural degeneration. Projects intended to refine and enhance diagnosis of psychiatric disorders such as anxiety, depression, and eating disorders include development of specialized paradigms to target dysfunctional neurocircuitry such as emotional systems (amygdala and basal ganglia) and control and regulatory systems (cingulate and pre-frontal cortex). Comparison of before-treatment images with after-treatment images to inform models of both treatment and disease and investigation of the hypothesis that individual genetic and functional differences have predictive value for treatment options and outcome are currently underway. The lab has pioneered techniques for functional mapping of single patients, and operates an active clinical service for mapping individuals for neurosurgical planning, assessments of the neurocircuitry that underlie acquired or inherited disabilities and the mechanisms of neuroplasticity that restore lost functions are actively investigated using both groups and single subject studies. :

Proper citation: fMRI Research Center at Columbia (RRID:SCR_002658) Copy   

•   Source: SciCrunch Registry

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

Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information

Proper citation: Beijing: Short TR Study (RRID:SCR_003502) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/pro/Quiron-Valencia.html

Resting state datasets, including an anatomical as well as a resting state fMRI scan, collected from a community sample in Valencia, Spain. The first release includes data for 45 participants. Participants were instructed to keep their eyes open during the resting state scan, no visual stimulus was presented. The following data are released for every participant: * Scanner Type: Philips Achieva 3T-TX * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * At least one 6-minute resting state fMRI scan (R-fMRI), eyes open, no visual stimulus presented * Demographic Information

Proper citation: Quiron-Valencia Sample (RRID:SCR_003538) Copy   

•   Source: SciCrunch Registry

http://www.linked-neuron-data.org/

Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc.

Proper citation: Linked Neuron Data (RRID:SCR_003658) Copy   

•   Source: SciCrunch Registry

http://www.cs.tau.ac.il/~shlomito/tissue-net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Network visualizations in which the expression and predicted flux data are projected over the global human network. These network visualizations are accessible through the supplemental website using the publicly available Cytoscape software (Cline, Smoot et al. 2007). Since many high degree nodes exist in the network, special layouts are required to produce network visualizations that are readily interpretable. To this end we produced network visualizations in which hub nodes are repeated multiple times and hence layouts with a small number of edge crossings can be generated. Contains entries for brain compartments and brain pathways.

Proper citation: Network-based Prediction of Human Tissue-specific Metabolism (RRID:SCR_007392) Copy   

•   Source: SciCrunch Registry