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http://afni.nimh.nih.gov/afni/

Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.

Proper citation: Analysis of Functional NeuroImages (RRID:SCR_005927) Copy   

•   Source: SciCrunch Registry

http://afni.nimh.nih.gov/afni/doc/misc/AtlasMap

A sample script on how to map some numbers to brain regions, using the Talairach-Tournoux Atlas database. For example, put the value 0.379 in each hippocampus voxel, and the value 0.666 in each superior temporal gyrus voxel.

Proper citation: Mapping Data to the Talairach Atlas (RRID:SCR_005284) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/bash-rs-fcmri

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.

Proper citation: BASH4RfMRI (RRID:SCR_005970) Copy   

•   Source: SciCrunch Registry

http://www.ncbcs.org/biositemaps/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites.

Proper citation: Biositemaps (RRID:SCR_001976) Copy   

•   Source: SciCrunch Registry

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

Data set of addiction studies compiled by the NeuroImaging and Analysis Group (NIAG).

Proper citation: NIAG Addiction Data (RRID:SCR_015523) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/

National institute that is the largest scientific organization in the world dedicated to research focused on the understanding, treatment, and prevention of mental disorders and the promotion of mental health. NIMH envisions a world in which mental illnesses are prevented and cured. The mission of NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery and cure. For the Institute to continue fulfilling this vital public health mission, it must foster innovative thinking and ensure that a full array of novel scientific perspectives are used to further discovery in the evolving science of brain, behavior, and experience. In this way, breakthroughs in science can become breakthroughs for all people with mental illnesses. In support of this mission, NIMH will generate research and promote research training to fulfill the following four objectives: * Promote discovery in the brain and behavioral sciences to fuel research on the causes of mental disorders * Chart mental illness trajectories to determine when, where, and how to intervene * Develop new and better interventions that incorporate the diverse needs and circumstances of people with mental illnesses * Strengthen the public health impact of NIMH-supported research To reach these goals, the NIMH divisions and programs are designed to emphasize translational research spanning bench, to bedside, to practice. For targeted priorities and funding initiatives, please visit our division websites

Proper citation: National Institute of Mental Health (RRID:SCR_011431) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/

Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.

Proper citation: NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430) Copy   

•   Source: SciCrunch Registry

http://nidm.nidash.org/

Collection of specification documents that define extensions the the W3C PROV standard for the domain of human brain mapping. NIDM uses provenance information as a means to link components from different stages of the scientific research process from dataset descriptors and computational workflow, to derived data and publication.

Proper citation: Neuroimaging Data Model (RRID:SCR_013667) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/afni_3dsvm/

A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X.

Proper citation: 3dsvm (RRID:SCR_014083) Copy   

•   Source: SciCrunch Registry