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.