=====                              =====
fMRI Phantom QA Tools
Author: Syam Gadde (gadde@biac.duke.edu)
Based on scripts created by Gary Glover
and further recommendations from the
fBIRN Calibration working group
=====                              =====

The only system requirement is that you have Perl installed.
Other required utilities are included as static binaries
(see their copyrights/licenses in COPYRIGHTS).

Included is a phantom QA script that generates Weisskoff
plots and other QA measures.  All binaries are in the
"bin" subdirectory.  The following examples assume the
fBIRNPhantomUploadDist2007 directory is in your home
directory (~).  You can alternately add the "bin"
directory to your PATH and eliminate the full paths.

First, relevant image parameters should be extracted from
your image files into a .bxh or XCEDE file.  For example,
from dicom:
  ~/fBIRNPhantomUploadDist2007/bin/dicom2bxh *.dcm myfile.bxh
OR:
  ~/fBIRNPhantomUploadDist2007/bin/dicom2bxh --xcede *.dcm myfile.xml

Then run the phantom QA script on this .bxh or XCEDE file:
  ~/fBIRNPhantomUploadDist2007/bin/fmriqa_phantomqa.pl myfile.bxh [outputdir]
OR:
  ~/fBIRNPhantomUploadDist2007/bin/fmriqa_phantomqa.pl myfile.xml [outputdir]

If outputdir is missing, it writes to the same directory as the
input file.

fmriqa_phantomqa.pl also takes the following options:
  --timeselect timepoints   Use only these timepoints (default is to
                            ignore first 2 or 3 timepoints, whichever
                            leaves an even number of timepoints).
			    You can also use ranges A:B which means
			    all timepoints between and including A and B.
			    Missing A means start at 0, missing B means
			    end at the last timepoint.  Note: indexing is
			    zero(0)-based!
  --zselect slice           Use this slice (default is middle slice)
  --overwrite               Overwrite files in outputdir if they exist
  --verbose                 Give some diagnostic messages during execution
  --comment                 Add an optional comment to the QA
  --summaryonly             Just produce a summary on standard output
                            (doesn't write any files)

