DTI Gradient Table Creator — DTI Gradient Table Creator computes the correct gradient table (i.e., the list of vectors that describe the diffusion weighting directions to use for analysis) for DTI acquisitions on Philips MRI scanners.  The code computes the gradient table based on minimal user input, and provides a quick and easy method to determine the correct gradient table necessary to calculate diffusion tensors (i.e., for FA, color coded principal eigenvector, fiber tracking etc.)

Eprime Programs from Function BIRN Phase I Traveling Subjects — employed during the FBIRN traveling subjects’ study of 2003, a Function-BIRN led study to standardize and calibrate imaging data for multi-site MRI studies by examining the brains of five subjects at nine different scanning sites across America (also see Traveling Subjects data set). The software paradigms include: sensorimotor task; breath hold task; program for the resting scans; Serial Item Recognition Paradigm (Sternberg, or SIRP); Mismatch Negativity or MMN paradigm. These programs require the commercially available E-prime software from Psychology Software Tools, Inc. (http://pstnet.com/products/e-prime/).

EPrime Phase II — These are E-prime programs for presenting stimuli to, collecting responses, and analyzing behavior from subjects. They measure a range of cognitive processes and were used by the FBIRN sites in collecting the multi-site Phase II data of 2004-2005.

Function BIRN Stability Phantom QA Procedures — are used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans. The scans are performed on a 17cm spherical phantom filled with an agar gel. The scans consist of 200 separate image volumes captured over roughly a 10 minute interval. Post acquisition analyses consist of mean and standard deviation measurements, drift and percent fluctuation in signal, signal-to-noise (SNR), and signal-to-fluctuation-noise (SFNR) ratios calculated over all volumes.

B0 and eddy current correction code for diffusion MRI — Software tool (executable plus code) and recommendations for acquisition protocols to correct distortions in diffusion MR images generated by main magnetic field inhomogeneities and eddy currents.

Gradient non-linearity distortion correction — The goal of this software is to provide a 3D correction of image distortions in MRI data due to non-linearity of the magnetic fields from the imaging gradient coils.

The Human Imaging Database (HID) has been developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities. The HID is an extensible database management system that is comprised of three core components:

• Human Imaging Database Schema — may be customized to contain relevant information from particular sites without requiring modification to the schema itself. This information may include data about the experimental subjects, subject assessments and demographics, acquired data, protocols, and annotations or statistics (metadata) normally included with a study.
• Clinical Assessment Layout Manager — helps incorporate online clinical assessment entry forms.
• Human Imaging Database Graphical User Interface — allows for the management of subjects and experiments.

Cell Centered Database (CCDB) — is an Internet databases for cellular imaging data. The CCDB houses structural and protein distribution information derived from confocal, electron microscopy and multiphoton microscopy. Designed to store and manage cell level information from tissue, cultured cells, and subcellular fractions, the CCDB models the entire process of reconstruction, from specimen preparation to segmentation and analysis.

XNAT — The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimagi ng and related data. XNAT includes a secure database backend and a rich web-based user interface.

The BIRN lexically-enhanced ontology (BIRNLex) — The BIRNLex ontology consists of a series of modules describing the important objects and processes within the biomedical research domains BIRN researchers require to provide semantically explict annotations for the data they intend to expose for federated querying via the BIRN Mediator. BIRN data sources include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer's disease or schizophrenia. The BIRN infrastructural tools enable BIRN scientists adding data to these repositories to map the terms they use to represent neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance into the BIRNLex common semantic framework. In this sense, BIRNLex is a critical component of the BIRN infrastructure via which the disparate data structures used by participating BIRN labs can be made collectively searchable within a shared ontological framework. The lexical enhancements consist of the variety of supporting elements associated with each BIRNLex semantic element. For instance, neuroanatomical region classes include common synonyms used across the field of neuroscience. Classes also include cross-references to synonymous items from other common terminologies covering the same semantic domain. This makes it possible for BIRNLex to be used to federate data sets previously annotated with those extant knowledge sources. BIRNLex classes also include consensus definitions and various curatorial properties required to track the version of the ontology. BIRNLex is primarily made available as a collection of OWL modules all imported via the main BIRNLex OWL file. The following page maintaned by the BIRN Ontology Task Force includes additional information both on the ontological engineering design practice used to curate BIRNLex, as well as additional ways in which to view and search the BIRNLex content. To browse and search the BIRNLex, visit the OntologEZ browser. BIRNLex is now available through the NCBO BioPortal.

Mouse Tissue Lineage Hierarchy — facilitates access to gene expression data in the Mouse Genome Informatics Database and the 2D and 3D gene expression database of EMAGE, by linking each anatomical feature during mouse development with the developmental history for each anatomical component.

XML-Based Clinical Experiment Data Exchange Schema (XCEDE) — provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes typical clinical information into five general hierarchical levels: project, study, subject, visit, and series.

BXH/XCEDE Tools — A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. These descriptors are "wrappers" of the original, unadulterated image data files, and provide a standard interface to image data and other metadata extracted from the image headers. Tools to create and use XML "event" descriptors for representing stimulus presentation and other time-based data are also provided.

XCEDE SPM Toolbox — was created to capture the results from activation maps using the XCEDE schema. The toolbox supports SPM99 and SPM2 statistical structures and has been tested on SUN, LINUX, and Microsoft Windows operating systems to capture PET and fMRI analysis results and the associated analysis model specifications.

BXH/XCEDE Tools — A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. These descriptors are "wrappers" of the original, unadulterated image data files, and provide a standard interface to image data and other metadata extracted from the image headers. Tools to create and use XML "event" descriptors for representing stimulus presentation and other time-based data are also provided.

CATNAP — CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program) is an end to end data processing pipeline for Philips PAR/REC Magnetic Resonance data files.  CATNAP performs motion correction for both diffusion and structural images using FSL FLIRT, adjusts the diffusion gradient directions for scanner settings (i.e., slice angulation, slice orientation, etc.) and motion correction (i.e., the rotational component of the applied transformation), and computes tensor and derived quantities (FA, MD, colormaps, eigenvalues etc).  The results are readily compatible with DTIStudio, FSL, and other tensor analysis packages.

FBIRN Image Processing Scripts — FIPS is a package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control. For more information, tutorials, and downloads, please see the publicly available BIRN Wiki: http://xwiki.nbirn.net:8080/xwiki/bin/view/Project-FIPS-Public/Home

FreeSurfer –- set of semi-automated tools for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface.

LONI Pipeline — provides a visual programming interface that allows researchers to link many independentlyhool.

The Human Imaging Database (HID) has been developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities. The HID is an extensible database management system that is comprised of three core components:

• Human Imaging Database Schema — may be customized to contain relevant information from particular sites without requiring modification to the schema itself. This information may include data about the experimental subjects, subject assessments and demographics, acquired data, protocols, and annotations or statistics (metadata) normally included with a study.
• Clinical Assessment Layout Manager — helps incorporate online clinical assessment entry forms.
• Human Imaging Database Graphical User Interface — allows for the management of subjects and experiments.

Cell Centered Database (CCDB) — is an Internet databases for cellular imaging data. The CCDB houses structural and protein distribution information derived from confocal, electron microscopy and multiphoton microscopy. Designed to store and manage cell level information from tissue, cultured cells, and subcellular fractions, the CCDB models the entire process of reconstruction, from specimen preparation to segmentation and analysis.

XNAT — The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface.

The BIRN lexically-enhanced ontology (BIRNLex) — The BIRNLex ontology consists of a series of modules describing the important objects and processes within the biomedical research domains BIRN researchers require to provide semantically explict annotations for the data they intend to expose for federated querying via the BIRN Mediator. BIRN data sources include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer's disease or schizophrenia. The BIRN infrastructural tools enable BIRN scientists adding data to these repositories to map the terms they use to represent neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance into the BIRNLex common semantic framework. In this sense, BIRNLex is a critical component of the BIRN infrastructure via which the disparate data structures used by participating BIRN labs can be made collectively searchable within a shared ontological framework. The lexical enhancements consist of the variety of supporting elements associated with each BIRNLex semantic element. For instance, neuroanatomical region classes include common synonyms used across the field of neuroscience. Classes also include cross-references to synonymous items from other common terminologies covering the same semantic domain. This makes it possible for BIRNLex to be used to federate data sets previously annotated with those extant knowledge sources. BIRNLex classes also include consensus definitions and various curatorial properties required to track the version of the ontology. BIRNLex is primarily made available as a collection of OWL modules all imported via the main BIRNLex OWL file. The following page maintaned by the BIRN Ontology Task Force includes additional information both on the ontological engineering design practice used to curate BIRNLex, as well as additional ways in which to view and search the BIRNLex content. To browse and search the BIRNLex, visit the OntologEZ browser. BIRNLex is now available through the NCBO BioPortal.

Mouse Tissue Lineage Hierarchy — facilitates access to gene expression data in the Mouse Genome Informatics Database and the 2D and 3D gene expression database of EMAGE, by linking each anatomical feature during mouse developmental levels: project, study, subject, visit, and series.

BXH/XCEDE Tools — A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. These descriptors are "wrappers" of the original, unadulterated image data files, and provide a standard interface to image data and other metadata extracted from the image headers. Tools to create and use XML "event" descriptors for representing stimulus presentation and other time-based data are also provided.

Defacer for Structural MRI — This algorithm, which is still under the validation phase, locates the subject's facial features and removes them without disturbing brain tissue. The algorithm was devised to work on T1-weighted structural MRI; it produces a defaced structural image, and an image of the applied mask. The code mri_deface produces a facial mask. The code mri_mask is then used to apply the mask to the original volume, resulting in a defaced structural image. For images in other modalities, the mask can be co-registered to theimage before application.

BrainGraph Editor — The BrainGraph Editor is used to create hierarchies out of information entered and classified by a user. This allows for organization and easy visualization and navigation through this type of information. The software can be used to create labels, tags, brief descriptions and metadata which are attached to the nodes in the hierarchy. Hierarchies may be visualized in either a Hyperbolic or Tree view and color may be added as additional information that may aid in visualizing a classification.

Mouse BIRN Atlasing Toolkit (MBAT) 2.0 BETA — This tool allows a user to view their data and offers the ability to interface with data offered by Mouse BIRN. This new release (2.0 BETA) includes several improvements and updates. Of particular note are the powerful query tools which access several data and information sources. MBAT 2.0 BETA improves and expands the previous query capability of MBAT. The query interface can be used for multiple data types and expands the primarily microarray data sources accessed in the previous version of MBAT to include image data from multiple sources.  In addition, MBAT 2.0 BETA can also be used to access information from web-resources including the BIRN Ontology Tool (Bonfire) and the Brain Architecture Management System (BAMS) at USC.

3D Slicer — open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data. Development of the Slicer is an ongoing collaboration between the MIT Artificial Intelligence Lab and the Surgical Planning Lab at Brigham & Women's Hospital, an affiliate of Harvard Medical School.

The BIRN lexically-enhanced ontology (BIRNLex) — The BIRNLex ontology consists of a series of modules describing the important objects and processes within the biomedical research domains BIRN researchers require to provide semantically explict annotations for the data they intend to expose for federated querying via the BIRN Mediator. BIRN data sources include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer's disease or schizophrenia. The BIRN infrastructural tools enable BIRN scientists adding data to these repositories to map the terms they use to represent neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance into the BIRNLex common semantic framework. In this sense, BIRNLex is a critical component of the BIRN infrastructure via which the disparate data structures used by participating BIRN labs can be made collectively searchable within a shared ontological framework. The lexical enhancements consist of the variety of supporting elements associated with each BIRNLex semantic element. For instance, neuroanatomical region classes include common synonyms used across the field of neuroscience. Classes also include cross-references to synonymous items from other common terminologies covering the same semantic domain. This makes it possible for BIRNLex to be used to federate data sets previously annotated with those extant knowledge sources. BIRNLex classes also include consensus definitions and various curatorial properties required to track the version of the ontology. BIRNLex is primarily made available as a collection of OWL modules all imported via the main BIRNLex OWL file. The following page maintaned by the BIRN Ontology Task Force includes additional information both on the ontological engineering design practice used to curate BIRNLex, as well as additional ways in which to view and search the BIRNLex content. To browse and search the BIRNLex, visit the OntologEZ browser. BIRNLex is now available through the NCBO BioPortal.

BrainGraph Editor — The BrainGraph Editor is used to create hierarchies out of information entered and classified by a user. This allows for organization and easy visualization and navigation through this type of information. The software can be used to create labels, tags, brief descriptions and metadata which are attached to the nodes in the hierarchy. Hierarchies may be visualized in either a Hyperbolic or Tree view and color may be added as additional information that may aid in visualizing a classification.

XML-Based Clinical Experiment Data Exchange Schema (XCEDE) — provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes typical clinical information into five general hierarchical levels: project, study, subject, visit, and series.

BXH/XCEDE Tools — A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. These descriptors are "wrappers" of the original, unadulterated image data files, and provide a standard interface to image data and other metadata extracted from the image headers. Tools to create and use XML "event" descriptors for representing stimulus presentation and other time-based data are also provided.