detect_adni_phantom - Detect ADNI phantom landmarks in phantom image
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).
- Write list of basic command line options to standard
- Write complete list of basic and advanced command line
options to standard output.
- Write list of command line options to standard output in
- Write man page source in 'nroff' markup to standard
- Write toolkit version to standard output.
- Write the current command line to standard output.
- --verbose-level <integer>
- Set verbosity level.
- --verbose, -v
- Increment verbosity level by 1 (deprecated; supported for
- --threads <integer>
- Set maximum number of parallel threads (for POSIX threads
- 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
- Do not assume standard orientation of the phantom, i.e.,
allow phantoms scanned upside-down. This makes detection of defective
phantoms less robust.
- 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 estimated affine transformation after each new
landmark is added.
- Refine outlier landmarks based on estimated transformation
after first sphere detection pass.
- Exclude outlier landmarks before fitting final
- 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]
- 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]
- 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.
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis,
Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
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