NAME

       detect_adni_phantom - Detect ADNI phantom landmarks in phantom image

SYNOPSIS

       detect_adni_phantom InputImage OutputXML

DESCRIPTION

       This  tool  detects  the locations of all spherical landmarks in a 3D image of the Magphan
       EMR051 structural imaging phantom (a.k.a. ADNI Phantom).

OPTIONS

   Global Toolkit Options (these are shared by all CMTK tools)
       --help
            Write list of basic command line options to standard output.

       --help-all
            Write complete list of basic and advanced command line options to standard output.

       --wiki
            Write list of command line options to standard output in MediaWiki markup.

       --man
            Write man page source in 'nroff' markup to standard output.

       --version
            Write toolkit version to standard output.

       --echo
            Write the current command line to standard output.

       --verbose-level <integer>
            Set verbosity level.

       --verbose, -v
            Increment verbosity level by 1 (deprecated; supported for backward compatibility).

       --threads <integer>
            Set maximum number of parallel threads (for POSIX threads and OpenMP).

   Phantom Detection Options
       --tolerant
            Be tolerant of issues such as partially truncated marker spheres. This should be used
            with  caution  only  when necessary, and both the phantom image and detection results
            should be carefully inspected to identify the source of detection problems and verify
            reliable results.

       --any-orientation
            Do  not  assume  standard  orientation  of  the phantom, i.e., allow phantoms scanned
            upside-down. This makes detection of defective phantoms less robust.

       --fallback-cnr-centroid
            Force a fallback to use centroid of CNR spheres rather than center of SNR sphere  for
            initial  orientation.  This  can be used when, for example, the SNR sphere has broken
            off but is positioned in a way that does not trigger the automatic fallback.

       --erode-snr <double>
            Erode SNR sphere by this distance prior to computing SNR estimate.  [Default: 10]

       --erode-cnr <double>
            Erode each CNR sphere by this distance prior to computing CNR estimate.  [Default: 5]

       --refine-xform
            Refine estimated affine transformation after each new landmark is added.

       --refine-outliers
            Refine outlier  landmarks  based  on  estimated  transformation  after  first  sphere
            detection pass.

       --exclude-outliers
            Exclude outlier landmarks before fitting final transformations.

       --no-bias-correct-spheres
            Disable  intensity  bias  field correction for each detected sphere. This will likely
            reduce accuracy of SNR/CNR estimates and also affect localication accuracy of smaller
            spheres, but may be helpful in extreme cases where bias correction fails completely.

   Output Options
       --write-labels <image-path>
            Output  label  image  path.  This  image  contains the mask of detected spheres, each
            labeled uniquely in their order in CMTK's ADNI  phantom  fiducial  table.   [Default:
            NONE]

       --write-rigid <transformation-path>
            Output  path  for  the  fitted rigid transformation from phantom space into RAS image
            standard space. This transformation defines where each sphere should be in the image.
            [Default: NONE]

       --write-affine <transformation-path>
            Output  path  for  the fitted affine transformation from phantom space into RAS image
            standard space. This is  the  closest  linear-fit  transformation,  and  as  such  it
            includes  scale and shear components not present in the fitted rigid transformations.
            Since these components  are  due  to  scanner  miscalibration  and  distortion,  this
            transformation  DOES  NOT  specify  the  correct  spehre  locations in the image, but
            rather, allows for quantification of scale miscalibration.  [Default: NONE]

AUTHORS

       Torsten Rohlfing, with contributions from Michael  P.  Hasak,  Greg  Jefferis,  Calvin  R.
       Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on
       Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data  Integration  Component.  From
       April  2009  through September 2011, CMTK development and maintenance was supported by the
       NIBIB under Grant EB008381.