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

A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools

Proper citation: GTRACT (RRID:SCR_009651) Copy   

•   Source: SciCrunch Registry

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

Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added.

Proper citation: IDeA Lab brain image processing suite (RRID:SCR_009495) Copy   

•   Source: SciCrunch Registry

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

A method for group-wise image registration by pairwisely registering similar images identified using graph theoretic techniques. Particularly, they use sparse coding to estimate image similarity measures among images to be registered, yielding asymmetric, group-wise image similarity measures for each image to others in the group.

Proper citation: Groupwise Image Registration Toolbox (RRID:SCR_009492) Copy   

•   Source: SciCrunch Registry

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

An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies.

Proper citation: HD Neuro-Informatics (RRID:SCR_009493) Copy   

•   Source: SciCrunch Registry

http://www.restfmri.net

A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files.

Proper citation: REST: a toolkit for resting-state fMRI (RRID:SCR_009641) Copy   

•   Source: SciCrunch Registry

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

Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction.

Proper citation: QCQP (RRID:SCR_009640) Copy   

•   Source: SciCrunch Registry

http://www.columbia.edu/~dx2103/brainimagescope.html

Software package for processing diffusion tensor imaging data. The following functions are included: 1. Converting imaging data in DICOME format to ANALYZE format 2. Extracting binary brain mask for quick scalp-removing 3. Correcting eddy-current induced distortion 4. Optimized tensor estimation based on noisy diffusion-weighted imaging (DWI) data 5. Scalp removal using a brain mask image 6. Corregistering imaging data and generating deformation field for mapping images from individual spaces to a template or target space 7. Spatial Normalization and Warping DTI 8. Fiber tracking 9. Clustering fiber tracts 10. Identifying brain ventricles and generating binary masks for the baseline and DW imaging data 11. Deriving diffusion anisotropy indices (DAIs) and principal directions (PD) and the corresponding color-coded PD-map.

Proper citation: DTI BrainImageScope (RRID:SCR_009559) Copy   

•   Source: SciCrunch Registry

http://cocomac.org/WWW/paxinos3D/index.html

An interactive interface of macaque stereotaxic atlas with a connectivity database, allowing integrated data analysis and mapping between 3D structures with database vocabularies. These Java-based tools are capable of reading stacks of polygons described in svg vector format and arrange them in 3D space so that the corresponding structures can be viewed and manipulated individually. An additional excel (currently v. 1997-2003) file maintains the structure abbreviations and their mapping to the terminology of databases that provide supplementary information. Here in particular we have manually drawn the cortical, striatal, thalamic and amygdaloid structures of the 151 frontal sections from the Rhesus Monkey Brain in Stereotactic Coordinates authored by Paxinos and colleagues in 1999. After loading the excel file and a set of the svg files, the view can be rotated, zoomed and individual brain structures be selected for identification and simple geometric measures. A stereotaxic grid is a display option. The abbreviations of the brain structures are mapped to entities recorded in the CoCoMac database of primate brain connectivity. Thereby one can retrieve mapping and connectivity information for the selected structure as text or connecting arrows.

Proper citation: CoCoMac-Paxinos3D viewer (RRID:SCR_009548) Copy   

•   Source: SciCrunch Registry

http://invizian.loni.usc.edu

A visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once ?bringing together brain image data from some of the world?s best neuroscience research teams. INVIZIAN empowers both researchers and students of neuroscience to explore and understand the human brain using a simple yet powerful user interface for neuroimaging data exploration and discovery. See a beautiful example of a cloud of individual brains tumbling around in the INVIZIAN interface in Vimeo (http://vimeo.com/67984681). Visit often to see how we are making continuing progress to make Invizian even more amazing.

Proper citation: INVIZIAN (RRID:SCR_009549) Copy   

•   Source: SciCrunch Registry

http://www.commerce.gov/

Executive department of the federal government concerned with promoting economic growth. Among its tasks are gathering economic and demographic data for business and government decision-making, and helping to set industrial standards.

Proper citation: U.S. Department of Commerce (RRID:SCR_009859) Copy   

•   Source: SciCrunch Registry

http://www.usgs.gov/

Scientific agency of the United States government. The scientists of the USGS study the landscape of the United States, its natural resources, and the natural hazards that threaten it. The organization's work spans the disciplines of biology, geography, geology, and hydrology.

Proper citation: U.S. Geological Survey (RRID:SCR_010168) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/BOF

An ontology of biodiversity of INPA

Proper citation: Biodiversity Ontology (RRID:SCR_010204) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/COGAT

Ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes.

Proper citation: Cognitive Atlas Ontology (RRID:SCR_010295) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CTCAE

A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI).

Proper citation: Common Terminology Criteria for Adverse Events (RRID:SCR_010296) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/cdao/

A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science

Proper citation: Comparative Data Analysis Ontology (RRID:SCR_010297) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CARELEX

Categories and terms used to classify content (documents, images, etc) in electronic content repositories for life science / BioPharma. Initial version contains content model for use with clinical trial electronic Trial Master Files or eTMF archives. A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. Recent changes include: addition of electronic signature support, medical imaging classifications.

Proper citation: Content Archive Resource Exchange Lexicon (RRID:SCR_010298) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/AAO

A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.

Proper citation: Amphibian Gross Anatomy Ontology (RRID:SCR_010291) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/HRDO

A core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database.

Proper citation: Disease core ontology applied to Rare Diseases (RRID:SCR_010308) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CPTH

Metathesaurus of current procedural terminalogy (CPT).

Proper citation: Current Procedural Terminalogy Hierarchy (RRID:SCR_010300) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IDODEN

An ontology for dengue fever.

Proper citation: Dengue Fever Ontology (RRID:SCR_010304) Copy   

•   Source: SciCrunch Registry