############################################################################## COPYRIGHT: University of California Berkeley 2006-2007 EMAIL: support@cirl.berkeley.edu Recon Tools: A collection of tools and libraries for reconstructing and undistorting MR image data developed at the University of California Berkeley's Helen Wills Neuroscience Institute Brain Imaging Center. For documentation, see https://cirl.berkeley.edu/view/BIC/ImagingTools #----------------------------------------------------------------------------- SUMMARY: The Recon Tools package provides a number of command-line tools for manipulating MR image data, as well as a code library of reusable components. The central types of objects in the recon-tools system are data readers, transformers, and writers. Image manipulation tools can be created by composing appropriate combinations of these core objects into a pipeline beginning with a reader, followed by a sequence of transformers (called Operations), and ending with a writer. Image data in the pipeline is represented by an Image object conforming to a conventional Image interface. #----------------------------------------------------------------------------- LIBRARY DEPENDENCIES: Recon Tools is written in Python 2.4, making use these additional libraries: numpy > 1.0 matplotlib > 0.87 #----------------------------------------------------------------------------- BUILDING/INSTALLING THE PYTHON WAY It is necessary to compile the phase surface unwrapping module included with Recon Tools before installing. To do so, type: python setup.py build sudo python setup.py install #----------------------------------------------------------------------------- USING MAKE (the iffy way): make install: installs tools, library, and documentation make tools-rpm: build an RPM for installing the tools and library make docs: generate some documentation from code make install-docs: install documentation (/usr/share/doc/recon-tools) make docs-rpm: build an RPM for install the documentation make test: run test suite make clean: remove all generated files #----------------------------------------------------------------------------- TESTING: To test your installation, a collection of example datasets and oplists is available at the CIRL wiki: https://cirl.berkeley.edu/twiki/pub/BIC/ReconTools/testsuite.tar.bz2 To use the testing util, type: tar jxf testsuite.tar.bz2 cd testsuite ./test.sh