detect_adni_phantom - Detect ADNI phantom landmarks in phantom
image
detect_adni_phantom InputImage OutputXML
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).
- --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).
- --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.
- --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]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg
Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
http://www.fsf.org/licensing/licenses/gpl.html
Report bugs at http://nitrc.org/projects/cmtk/
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.