Biomedical Informatics Research Network (BIRN) | Analysis and Processing Tools

Analysis and Processing Tools

The following BIRN tools allow you to analyze and process your data in scientifically meaningful ways:

BXH/XCEDE Tools – 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.
CATNAP – The Coregistration, Adjustment, and Tensor-solving, a Nicely Automated Program (CATNAP) 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).
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.
FBIRN Image Processing Scripts (FIPS) – 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.
FreeSurfer – FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
LONI Pipeline – The LONI Pipeline is a free workflow application primarily aimed at Neuroimaging Researchers. With the LONI Pipeline, users can create workflows that take advantage of all the greatest Neuroimaging tools available, quickly.
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.

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