How BIRN is organized

• BIRN Executive Committee
• Key Personnel
• Participating Institutions

What BIRN offers

• BIRN CC Tools Primer
• fBIRN Tools Primer
• mBIRN Tools Primer
• Mouse BIRN Tools Primer
• BIRN Data Repository

Who uses BIRN

• BIRN Coordinating Center
• Function BIRN
• Morphometry BIRN
• Mouse BIRN

Affiliated Sites

• NCRR
• NIH-CIT
• NDAR
• NA-MIC
• UK e-Science

BIRN Glossary

Copyright

BXH XCEDE Tools

Overview:

The BXH/XCEDE tools suite is designed for reading, writing and manipulating XML-based image and event data descriptors.

An XML-based BXH or XCEDE image descriptor provides a consistent, portable, easily-parsable descriptor for one or more data files, which can consist of raw data or remain encapsulated in their native format (i.e. DICOM, SIGNA, Analyze, etc.). The BXH/XCEDE header is image-format-agnostic, and stores important header information (such as byte order, dimensions, image position, acquisition parameters, etc.) to allow BXH/XCEDE-enabled tools to read, write, display, and manipulate the stored data.

New developments include an XML-based extension to describe "event" data, defined as (onset, duration) pairs, associated with appropriate metadata. This is currently used for describing stimulus/response data from task presentation software and for storing image QA measures.

This software suite incorporates a wide range of tools in the following categories:

BXH/XCEDE creation: These tools will create a BXH (or XCEDE, if the --xcede option is specified) XML file that "wraps" the image data in the various supported formats. Some of the important metadata in the image headers are extracted into the XML file using a standard naming scheme. In a typical installation, most of these tools are symbolically linked to the same executable -- the behavior of the tool is switched based on the name of the link. bxhabsorb attempts to autodetect the format of the input images, whereas the other tools assume a given input format.

BXH/XCEDE conversion tools: These tools convert from BXH or XCEDE into other image formats.

BXH/XCEDE manipulation tools: These tools manipulate the BXH or XCEDE file in various ways.

BXH/XCEDE QA tools: These tools perform QA (quality assurance) calculations and produce images, graphs, and/or XML data as output. fmriqa_phantomqa.pl and fmriqa_generate.pl produce an HTML report with various QA measures. fmriqa_phantomqa.pl was designed for fMRI images of the BIRN stability phantom, and fmriqa_generate.pl has been used for human fMRI data.

bxh_eventstats and related image processing and statistical tools: bxh_eventstats is an event-based epoch averaging tool. It collects event-synchronized "snippets" of the fMRI response, averages them, and optionally correlates them to a template hemodynamic response or to other averaged "snippets". The times of the chosen fragments are selected by querying XML events files for events matching given characteristics.

BXH/XCEDE XML events file creation tools: These tools are used to create the XML events files used by bxh_eventstats and other tools.

BXH/XCEDE XML events file manipulation tools: These tools are used to manipulate XML events files.

Manual: A manual describing the BXH tools can be found here

CONTRIBUTORS/AUTHORS: This software was developed primarily by Syam Gadde (Duke-UNC Brain Imaging and Analysis Center, Duke University). The original implementation of bxh2analyze was written by Jeff Hoerle (Duke-UNC Brain Imaging and Analysis Center, Duke University).

REFERENCES FOR THE SOFTWARE: Syam Gadde, Charles R. Michelich, James Voyvodic (2004) "An XML-based Data Access Interface for Image Analysis and Visualization Software." Annual Meeting of the Organization for Human Brain Mapping, Budapest, Hungary. 2004. (poster)

TECHNICAL CONTACT: Syam Gadde gadde@biac.duke.edu

ACKNOWLEDGEMENTS AND FUNDING SOURCES: The development of this software has been supported by the National Center for Research Resources (NCRR) at the National Institutes of Health (NIH), via two testbeds of the the Biomedical Informatics Research Network (BIRN, http://www.nbirn.net): the Brain Morphometry BIRN (3M01RR00030), and the Functional Imaging Research of Schizophrenia Testbed (FIRST) BIRN, (BIRN004). This package contains programs from the external packages ImageMagick, gnuplot, and the Perl module File::Which. The copyrights for these tools are listed in the file COPYRIGHTS available in the extracted software distribution.