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http://www.brain.northwestern.edu/index.html
The Cognitive Neurology and Alzheimer's Disease Center (CNADC) is a multidisciplinary organization dedicated to conducting research to discover how the brain coordinates mental functions such as memory, language, attention, and emotion; transferring the benefits of this research to patients with brain diseases that impair cognitive function; and training researchers and clinicians who want to work in this field. The CNADC's mission is to investigate the neurological basis of cognitive function, to elucidate causes of dementia, and to ensure that the patients and their families are the beneficiaries of resultant discoveries. * Clinical Services: Neurobehavior and Memory Health Clinical Services * Annual Grant Opportunities: Annual Core Pilot Project Funding Opportunities * Research Areas & Faculty: Alzheimer's Disease / Primary Progressive Aphasia / Frontal Dementia, Brain Endowment (Brains are permanently stored, and requests for tissue for research purposes are submitted to Dr. Bigio for review by the Northwestern Alzheimer's Disease Center); Cognitive Brain Mapping Group, Volunteer For A Study * Fellowships: Neuropathology Fellowship, Behavioral Neurology & Neuropsychiatry Fellowship * Training Programs: Mechanisms of Aging and Dementia (M.A.D.) Training Program; Training Program in the Neuroscience of Human Cognition
Proper citation: Northwestern University Cognitive Neurology and Alzheimers Disease Center (RRID:SCR_012747) Copy
https://github.com/ABCD-STUDY/DEAP
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Proper citation: NeMOarchive (RRID:SCR_016152) Copy
http://www.nitrc.org/projects/vdb/
Virtual resource for neuroscience.
Proper citation: Virtual Digital Brain (RRID:SCR_016265) Copy
http://ielvis.pbworks.com/w/page/116347253/FrontPage
Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization.
Proper citation: iELVis (RRID:SCR_016109) Copy
Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis.
Proper citation: International Initiative for Traumatic Brain Injury Research (RRID:SCR_016237) Copy
https://github.com/nighres/nighres
Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.
Proper citation: Nighres (RRID:SCR_016287) Copy
http://www.nitrc.org/projects/mica/
Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.
Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy
Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers.
Proper citation: Canadian Open Neuroscience Platform (RRID:SCR_016433) Copy
http://www.nitrc.org/projects/uf2c/
Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters.
Proper citation: User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) Copy
https://doi.org/10.1016/j.neuroimage.2018.07.046
Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.
Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) Copy
https://www.neuronexus.com/files/catalog/NeuroNexus-2023ProbeDesignCatalog.pdf
Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications.
Proper citation: Neuronexus: Neural Probe A1x16-3mm-100-703 (RRID:SCR_016678) Copy
http://jefferis.github.io/nat/
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy
https://github.com/NeurophysVis/SpectraVis
Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity.
Proper citation: SpectraVis (RRID:SCR_016691) Copy
http://www.neuro.uni-jena.de/cat/
Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.
Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) Copy
https://github.com/PatternRecognition/OpenBMI
Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time.
Proper citation: OpenBMI (RRID:SCR_016876) Copy
Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.
Proper citation: INCF-Neurobot (RRID:SCR_017004) Copy
Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts.
Proper citation: Empenn (RRID:SCR_017074) Copy
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) Copy
Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz.
Proper citation: Prism Clinical Imaging (RRID:SCR_016977) Copy
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