BXH/XCEDE tools documentation

This is a suite of tools written to read, write, and manipulate image data using XML-based BXH or XCEDE headers. Any tool that reads BXH will read XCEDE, and vice-versa.

The help messages for the various tools are linked below.

BXH/XCEDE creation tools

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".

Various screeds on topics related to bxh_eventstats are listed here:

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.