NAME
Atropos  part of ANTS registration suite
DESCRIPTION
COMMAND:

./Atropos

A finite mixture modeling (FMM) segmentation approach with possibilities for
specifying prior constraints. These prior constraints include the specification
of a prior label image, prior probability images (one for each class), and/or an
MRF prior to enforce spatial smoothing of the labels. Similar algorithms include
FAST and SPM.
OPTIONS:

d, imagedimensionality 2/3/4

 This option forces the image to be treated as a specifieddimensional image. If
not specified, Atropos tries to infer the dimensionality from the first input
image.

a, intensityimage [intensityImage,<adaptiveSmoothingWeight>]

 One or more scalar images is specified for segmentation using the
a/intensityimage option. For segmentation scenarios with no prior
information, the first scalar image encountered on the command line is used to
order labelings such that the class with the smallest intensity signature is
class '1' through class 'N' which represents the voxels with the largest
intensity values. The optional adaptive smoothing weight parameter is applicable
only when using prior label or probability images. This scalar parameter is to
be specified between [0,1] which smooths each labeled region separately and
modulates the intensity measurement at each voxel in each intensity image
between the original intensity and its smoothed counterpart. The smoothness
parameters are governed by the b/bspline option.

b, bspline [<numberOfLevels=6>,<initialMeshResolution=1x1x...>,<splineOrder=3>]

 If the adaptive smoothing weights are > 0, the intensity images are smoothed in
calculating the likelihood values. This is to account for subtle intensity
differences across the same tissue regions.
 i, initialization Random[numberOfClasses]

Otsu[numberOfClasses]
KMeans[numberOfClasses,<clusterCenters(in ascending order and for first intensity image only)>]
PriorProbabilityImages[numberOfClasses,fileSeriesFormat(index=1 to numberOfClasses) or vectorImage,priorWeighting,<priorProbabilityThreshold>]
PriorLabelImage[numberOfClasses,labelImage,priorWeighting]

To initialize the FMM parameters, one of the following options must be
specified. If one does not have prior label or probability images we recommend
using kmeans as it is typically faster than otsu and can be used with
multivariate initialization. However, since a Euclidean distance on the inter
cluster distances is used, one might have to appropriately scale the additional
input images. Random initialization is meant purely for intellectual curiosity.
The prior weighting (specified in the range [0,1]) is used to modulate the
calculation of the posterior probabilities between the likelihood*mrfprior and
the likelihood*mrfprior*prior. For specifying many prior probability images for
a multilabel segmentation, we offer a minimize usage option (see m). With that
option one can specify a prior probability threshold in which only those pixels
exceeding that threshold are stored in memory.
 p, posteriorformulation Socrates[<useMixtureModelProportions=1>]

Plato[<useMixtureModelProportions=1>]
Aristotle[<useMixtureModelProportions=1>]

Different posterior probability formulations are possible which include the
following: Socrates: posteriorProbability =
(spatialPrior)^priorWeight*(likelihood*mrfPrior)^(1priorWeight), Plato:
posteriorProbability = 1.0, Aristotle: posteriorProbability = 1.0,

x, maskimage maskImageFilename

 The image mask (which is required) defines the region which is to be labeled by
the Atropos algorithm.

c, convergence [<numberOfIterations=5>,<convergenceThreshold=0.001>]

 Convergence is determined by calculating the mean maximum posterior probability
over the region of interest at each iteration. When this value decreases or
increases less than the specified threshold from the previous iteration or the
maximum number of iterations is exceeded the program terminates.
 k, likelihoodmodel Gaussian

HistogramParzenWindows[<sigma=1.0>,<numberOfBins=32>]
ManifoldParzenWindows[<pointSetSigma=1.0>,<evaluationKNeighborhood=50>,<CovarianceKNeighborhood=0>,<kernelSigma=0>]
LogEuclideanGaussian

Both parametric and nonparametric options exist in Atropos. The Gaussian
parametric option is commonly used (e.g. SPM & FAST) where the mean and standard
deviation for the Gaussian of each class is calculated at each iteration. Other
groups use nonparametric approaches exemplified by option 2. We recommend using
options 1 or 2 as they are fairly standard and the default parameters work
adequately.

m, mrf [<smoothingFactor=0.3>,<radius=1x1x...>]

 Markov random field (MRF) theory provides a general framework for enforcing
spatially contextual constraints on the segmentation solution. The default
smoothing factor of 0.3 provides a moderate amount of smoothing. Increasing this
number causes more smoothing whereas decreasing the number lessens the
smoothing. The radius parameter specifies the mrf neighborhood.

o, output [classifiedImage,<posteriorProbabilityImageFileNameFormat>]

 The output consists of a labeled image where each voxel in the masked region is
assigned a label from 1, 2, ..., N. Optionally, one can also output the
posterior probability images specified in the same format as the prior
probability images, e.g. posterior%02d.nii.gz (Cstyle file name formatting).

u, minimizememoryusage (0)/1

 By default, memory usage is not minimized, however, if this is needed, the
various probability and distance images are calculated on the fly instead of
being stored in memory at each iteration. Also, if prior probability images are
used, only the nonnegligible pixel values are stored in memory.
<VALUES>: 0
 w, winsorizeoutliers BoxPlot[<lowerPercentile=0.25>,<upperPercentile=0.75>,<whiskerLength=1.5>]

GrubbsRosner[<significanceLevel=0.05>,<winsorizingLevel=0.10>]

To remove the effects of outliers in calculating the weighted mean and weighted
covariance, the user can opt to remove the outliers through the options
specified below.

e, useeuclideandistance (0)/1

 Given prior label or probability images, the labels are propagated throughout
the masked region so that every voxel in the mask is labeled. Propagation is
done by using a signed distance transform of the label. Alternatively,
propagation of the labels with the fast marching filter respects the distance
along the shape of the mask (e.g. the sinuous sulci and gyri of the cortex.
<VALUES>: 0

l, labelpropagation whichLabel[lambda=0.0,<boundaryProbability=1.0>]

 The propagation of each prior label can be controlled by the lambda and boundary
probability parameters. The latter parameter is the probability (in the range
[0,1]) of the label on the boundary which increases linearly to a maximum value
of 1.0 in the interior of the labeled region. The former parameter dictates the
exponential decay of probability propagation outside the labeled region from the
boundary probability, i.e. boundaryProbability*exp( lambda * distance ).

h

 Print the help menu (short version).
<VALUES>: 0

help

 Print the help menu.
<VALUES>: 1, 0