Open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data.

A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.

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.

The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment.

BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.

A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.

Status: In testing (forecast for October 2009)
The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN [...]

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.

The 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.

Helps incorporate online clinical assessment entry forms.

The Upload scripts work in concert with the GridFTP servers, XCEDE, and the standardized data hierarchies to put data onto the GridFTP servers and link it to the appropriate database.

This algorithm, which is still under the validation phase, locates the subject’s facial features and removes them without disturbing brain tissue.

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.

These are E-prime programs for presenting stimuli to, collecting responses, and analyzing behavior from subjects.

Employed during the FBIRN traveling subjects’ study of 2003, this is 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.

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.

FIRE (coming in 2010) is an integrated suite of tools to put your data on a gridFTP set of servers, link it to a database which is automatically federated, to be able to retrieve it from multiple sites, with the data wrapped in XCEDE (XML) wrappers.

Set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface.

Used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans.

Grid Account Management Architecture, GAMA, provides an end-to-end security infrastructure suitable for multi-institution collaborations with support for grid computing, cloud computing, and web portals.

The Globus clients software provides MyProxy, GSI security, GridFTP, UberFTP, and RLS client software that enables users and applications to interact with BIRN operated MyProxy, GridFTP, and RLS servers.

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.

GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks.

Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities.

The Large Deformation Diffeomorphic Metric Mapping (LDDMM) tool is an application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes.

The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats.

The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.

Provides a visual programming interface that allows researchers to link many independently developed analysis programs into a processing “pipeline.”

The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.

MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.

MRI Studio is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration.

MyProxy is an online credential repository. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network.

NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.

REM registers N-D image pairs that may contain topological differences.

Captures the results from activation maps using the XCEDE schema.

Provides an extensive metadata hierarchy for describing and documenting research and clinical studies.

The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data.

Open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data.

A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.

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.

The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment.

BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.

A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.

Status: In testing (forecast for October 2009)
The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN [...]

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.

The 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.

Helps incorporate online clinical assessment entry forms.

The Upload scripts work in concert with the GridFTP servers, XCEDE, and the standardized data hierarchies to put data onto the GridFTP servers and link it to the appropriate database.

This algorithm, which is still under the validation phase, locates the subject’s facial features and removes them without disturbing brain tissue.

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.

These are E-prime programs for presenting stimuli to, collecting responses, and analyzing behavior from subjects.

Employed during the FBIRN traveling subjects’ study of 2003, this is 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.

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.

FIRE (coming in 2010) is an integrated suite of tools to put your data on a gridFTP set of servers, link it to a database which is automatically federated, to be able to retrieve it from multiple sites, with the data wrapped in XCEDE (XML) wrappers.

Set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface.

Used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans.

Grid Account Management Architecture, GAMA, provides an end-to-end security infrastructure suitable for multi-institution collaborations with support for grid computing, cloud computing, and web portals.

The Globus clients software provides MyProxy, GSI security, GridFTP, UberFTP, and RLS client software that enables users and applications to interact with BIRN operated MyProxy, GridFTP, and RLS servers.

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.

GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks.

Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities.

The Large Deformation Diffeomorphic Metric Mapping (LDDMM) tool is an application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes.

The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats.

The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.

Provides a visual programming interface that allows researchers to link many independently developed analysis programs into a processing “pipeline.”

The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.

MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.

MRI Studio is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration.

MyProxy is an online credential repository. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network.

NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.

REM registers N-D image pairs that may contain topological differences.

Captures the results from activation maps using the XCEDE schema.

Provides an extensive metadata hierarchy for describing and documenting research and clinical studies.

The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data.

Open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data.

A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.

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.

The BIRN_ID generator can be used to assign a unique ID to subjects in any type of experiment.

BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.

A suite of tools designed to read, write and manipulate XML descriptors using the BXH or XCEDE schemas. This tool is REQUIRED for many other FBIRN tools.

Status: In testing (forecast for October 2009)
The Capability Registry capability enables the BIRN community to discover using a central authoritative repository what capabilities the BIRN [...]

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.

The 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.

Helps incorporate online clinical assessment entry forms.

The Upload scripts work in concert with the GridFTP servers, XCEDE, and the standardized data hierarchies to put data onto the GridFTP servers and link it to the appropriate database.

This algorithm, which is still under the validation phase, locates the subject’s facial features and removes them without disturbing brain tissue.

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.

These are E-prime programs for presenting stimuli to, collecting responses, and analyzing behavior from subjects.

Employed during the FBIRN traveling subjects’ study of 2003, this is 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.

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.

FIRE (coming in 2010) is an integrated suite of tools to put your data on a gridFTP set of servers, link it to a database which is automatically federated, to be able to retrieve it from multiple sites, with the data wrapped in XCEDE (XML) wrappers.

Set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface.

Used to verify and measure the scanner stability during a typical fMRI scanning sequence during routine quality assurance scans.

Grid Account Management Architecture, GAMA, provides an end-to-end security infrastructure suitable for multi-institution collaborations with support for grid computing, cloud computing, and web portals.

The Globus clients software provides MyProxy, GSI security, GridFTP, UberFTP, and RLS client software that enables users and applications to interact with BIRN operated MyProxy, GridFTP, and RLS servers.

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.

GridFTP is a high-performance, secure, reliable data transfer protocol optimized for high-bandwidth wide-area networks.

Developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities.

The Large Deformation Diffeomorphic Metric Mapping (LDDMM) tool is an application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes.

The Debabeler is a robust and extensible tool used to create and customize translations between medical image file formats.

The LONI Inspector is a Java application for reading, displaying, searching, comparing, and exporting metadata from AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI files.

Provides a visual programming interface that allows researchers to link many independently developed analysis programs into a processing “pipeline.”

The LONI Provenance Editor is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

An interactive tool for stereotaxic brain data visualization. LOVE is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.

MBAT provides a workflow environment bringing together online resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.

MRI Studio is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration.

MyProxy is an online credential repository. You can store X.509 proxy credentials in the MyProxy repository, protected by a passphrase, for later retrieval over the network.

NeuroLex is built from a core OWL ontology, originally built from BIRNLex, in a modular fashion, with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, function and dysfunction.

REM registers N-D image pairs that may contain topological differences.

Captures the results from activation maps using the XCEDE schema.

Provides an extensive metadata hierarchy for describing and documenting research and clinical studies.

The Extensible Neuroimaging Archive Toolkit (XNAT) is an open source software platform designed to facilitate management and exploration of neuroimaging and related data.