bionic (1) antsRegistration.1.gz

Provided by: ants_2.2.0-1ubuntu1_amd64 bug

NAME

       antsRegistration - part of ANTS registration suite

DESCRIPTION

   COMMAND:
              antsRegistration

              This  program  is  a  user-level registration application meant to utilize ITKv4-only classes. The
              user can specify any number of "stages" where a stage consists of a transform;  an  image  metric;
              and  iterations, shrink factors, and smoothing sigmas for each level. Note that explicitly setting
              the dimensionality, metric, transform, output, convergence, shrink-factors,  and  smoothing-sigmas
              parameters is mandatory.

   OPTIONS:
       --version

              Get Version Information.

       -d, --dimensionality 2/3

              This  option forces the image to be treated as a specified-dimensional image. If not specified, we
              try to infer the dimensionality from the input image.

       -o, --output outputTransformPrefix

              [outputTransformPrefix,<outputWarpedImage>,<outputInverseWarpedImage>]

              Specify the output transform prefix (output format is .nii.gz ). Optionally,  one  can  choose  to
              warp the moving image to the fixed space and, if the inverse transform exists, one can also output
              the warped fixed image. Note that only the images specified in the first metric call  are  warped.
              Use antsApplyTransforms to warp other images using the resultant transform(s).

       -j, --save-state saveSateAsTransform

              Specify the output file for the current state of the registration. The state file is written to an
              hdf5 composite file. It is specially usefull if we want  to  save  the  current  state  of  a  SyN
              registration  to the disk, so we can load and restore that later to continue the next registration
              process directly started from the last saved state. The output file of this flag is  the  same  as
              the  write-composite-transform,  unless  the  last transform is a SyN transform. In that case, the
              inverse displacement field of the SyN transform is also added to the output  composite  transform.
              Again  notice  that  this  file cannot be treated as a transform, and restore-state option must be
              used to load the written file by this flag.

       -k, --restore-state restoreStateAsATransform

              Specify the initial state of the registration which get immediately used  to  directly  initialize
              the  registration  process.  The flag is mutually exclusive with other intialization flags.If this
              flag is used, none of the initial-moving-transform and initial-fixed-transform cannot be used.

       -a, --write-composite-transform 1/(0)

              Boolean specifying whether or not the composite transform (and its inverse, if it  exists)  should
              be written to an hdf5 composite file. This is false by default so that only the transform for each
              stage is written to file.  <VALUES>: 0

       -p, --print-similarity-measure-interval <unsignedIntegerValue>

              Prints out the CC similarity metric measure between the full-size input fixed and the  transformed
              moving  images  at  each  iteration  a  value  of  0  (the  default) indicates that the full scale
              computation should not take placeany value greater than 0 represents the interval  of  full  scale
              metric computation.  <VALUES>: 0

       --write-interval-volumes <unsignedIntegerValue>

              Writes  out the output volume at each iteration. It helps to present the registration process as a
              short movie a value of 0 (the default) indicates that this option should not take  placeany  value
              greater  than  0  represents  the interval between the iterations which outputs are written to the
              disk.  <VALUES>: 0

       -z, --collapse-output-transforms (1)/0

              Collapse output transforms. Specifically, enabling this option combines  all  adjacent  transforms
              wherepossible.  All  adjacent  linear  transforms  are  written  to  disk in the forman itk affine
              transform (called xxxGenericAffine.mat).  Similarly, all adjacent  displacement  field  transforms
              are   combined   when   written   to  disk  (e.g.  xxxWarp.nii.gz  and  xxxInverseWarp.nii.gz  (if
              available)).Also, an output composite transform including the collapsed transforms is  written  to
              the disk (called outputCollapsed(Inverse)Composite).  <VALUES>: 1

       -i, --initialize-transforms-per-stage (1)/0

              Initialize  linear transforms from the previous stage. By enabling this option, the current linear
              stage transform is directly intialized from the previous stage's  linear  transform;  this  allows
              multiple  linear stages to be run where each stage directly updates the estimated linear transform
              from the previous stage. (e.g. Translation -> Rigid -> Affine).  <VALUES>: 0

       -n, --interpolation Linear
              NearestNeighbor                                       MultiLabel[<sigma=imageSpacing>,<alpha=4.0>]
              Gaussian[<sigma=imageSpacing>,<alpha=1.0>] BSpline[<order=3>] CosineWindowedSinc WelchWindowedSinc
              HammingWindowedSinc LanczosWindowedSinc GenericLabel[<interpolator=Linear>]

              Several interpolation options are available in ITK. These have all been made available.  Currently
              the  interpolator  choice  is  only  used  to  warp  (and  possibly inverse warp) the final output
              image(s).

       -g, --restrict-deformation PxQxR

              This option allows the user to restrict the optimization of the displacement  field,  translation,
              rigid  or  affine  transform  on  a  per-component  basis.  For example, if one wants to limit the
              deformation or rotation of 3-D volume to the first two dimensions, this is possible by  specifying
              a  weight  vector  of '1x1x0' for a deformation field or '1x1x0x1x1x0' for a rigid transformation.
              Low-dimensional restriction only works if there are no preceding transformations.

       -q, --initial-fixed-transform initialTransform
              [initialTransform,<useInverse>] [fixedImage,movingImage,initializationFeature]

              Specify the initial fixed transform(s) which  get  immediately  incorporated  into  the  composite
              transform.  The order of the transforms is stack-esque in that the last transform specified on the
              command line is the first to be applied. In addition to initialization with  ITK  transforms,  the
              user  can  perform  an initial translation alignment by specifying the fixed and moving images and
              selecting an initialization feature. These features include using  the  geometric  center  of  the
              images (=0), the image intensities (=1), or the origin of the images (=2).

       -r, --initial-moving-transform initialTransform
              [initialTransform,<useInverse>] [fixedImage,movingImage,initializationFeature]

              Specify  the  initial  moving  transform(s)  which get immediately incorporated into the composite
              transform. The order of the transforms is stack-esque in that the last transform specified on  the
              command  line  is  the first to be applied. In addition to initialization with ITK transforms, the
              user can perform an initial translation alignment by specifying the fixed and  moving  images  and
              selecting  an  initialization  feature.  These  features include using the geometric center of the
              images (=0), the image intensities (=1), or the origin of the images (=2).

       -m,                                                                                              --metric
              CC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]

              MI[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
              Mattes[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
              MeanSquares[fixedImage,movingImage,metricWeight,radius=NA,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
              Demons[fixedImage,movingImage,metricWeight,radius=NA,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
              GC[fixedImage,movingImage,metricWeight,radius=NA,<samplingStrategy={None,Regular,Random}>,<samplingPercentage=[0,1]>]
              ICP[fixedPointSet,movingPointSet,metricWeight,<samplingPercentage=[0,1]>,<boundaryPointsOnly=0>]
              PSE[fixedPointSet,movingPointSet,metricWeight,<samplingPercentage=[0,1]>,<boundaryPointsOnly=0>,<pointSetSigma=1>,<kNeighborhood=50>]
              JHCT[fixedPointSet,movingPointSet,metricWeight,<samplingPercentage=[0,1]>,<boundaryPointsOnly=0>,<pointSetSigma=1>,<kNeighborhood=50>,<alpha=1.1>,<useAnisotropicCovariances=1>]
              IGDM[fixedImage,movingImage,metricWeight,fixedMask,movingMask,<neighborhoodRadius=0x0>,<intensitySigma=0>,<distanceSigma=0>,<kNeighborhood=1>,<gradientSigma=1>]

              These  image  metrics  are  available---  CC:  ANTS  neighborhood  cross  correlation,  MI: Mutual
              information, Demons: (Thirion),  MeanSquares,  and  GC:  Global  Correlation.  The  "metricWeight"
              variable is used to modulate the per stage weighting of the metrics. The metrics can also employ a
              sampling strategy defined by a sampling percentage. The sampling strategy defaults to 'None'  (aka
              a dense sampling of one sample per voxel), otherwise it defines a point set over which to optimize
              the metric. The point set can be on a regular lattice or  a  random  lattice  of  points  slightly
              perturbed  to  minimize  aliasing artifacts.  samplingPercentage defines the fraction of points to
              select from the domain. In addition, three point  set  metrics  are  available:  Euclidean  (ICP),
              Point-set expectation (PSE), and Jensen-Havrda-Charvet-Tsallis (JHCT).

       -t, --transform Rigid[gradientStep]
              Affine[gradientStep]             CompositeAffine[gradientStep]            Similarity[gradientStep]
              Translation[gradientStep]                                BSpline[gradientStep,meshSizeAtBaseLevel]
              GaussianDisplacementField[gradientStep,updateFieldVarianceInVoxelSpace,totalFieldVarianceInVoxelSpace]
              BSplineDisplacementField[gradientStep,updateFieldMeshSizeAtBaseLevel,totalFieldMeshSizeAtBaseLevel,<splineOrder=3>]
              TimeVaryingVelocityField[gradientStep,numberOfTimeIndices,updateFieldVarianceInVoxelSpace,updateFieldTimeVariance,totalFieldVarianceInVoxelSpace,totalFieldTimeVariance]
              TimeVaryingBSplineVelocityField[gradientStep,velocityFieldMeshSize,<numberOfTimePointSamples=4>,<splineOrder=3>]
              SyN[gradientStep,updateFieldVarianceInVoxelSpace,totalFieldVarianceInVoxelSpace]
              BSplineSyN[gradientStep,updateFieldMeshSizeAtBaseLevel,totalFieldMeshSizeAtBaseLevel,<splineOrder=3>]
              Exponential[gradientStep,updateFieldVarianceInVoxelSpace,velocityFieldVarianceInVoxelSpace,<numberOfIntegrationSteps>]
              BSplineExponential[gradientStep,updateFieldMeshSizeAtBaseLevel,velocityFieldMeshSizeAtBaseLevel,<numberOfIntegrationSteps>,<splineOrder=3>]

              Several  transform  options  are  available.  The  gradientStep  or learningRate characterizes the
              gradient descent optimization and is scaled appropriately  for  each  transform  using  the  shift
              scales  estimator.  Subsequent  parameters  are  transform-specific and can be determined from the
              usage. For the B-spline transforms one can also specify the smoothing in terms of spline  distance
              (i.e.  knot spacing).

       -c, --convergence MxNxO
              [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]

              Convergence  is  determined from the number of iterations per level and is determined by fitting a
              line to the normalized energy profile of the last N iterations (where N is specified by the window
              size) and determining the slope which is then compared with the convergence threshold.

       -s, --smoothing-sigmas MxNxO...

              Specify  the sigma of gaussian smoothing at each level. Units are given in terms of voxels ('vox')
              or physical spacing ('mm'). Example usage is '4x2x1mm' and '4x2x1vox' where no units implies voxel
              spacing.

       -f, --shrink-factors MxNxO...

              Specify the shrink factor for the virtual domain (typically the fixed image) at each level.

       -u, --use-histogram-matching

              Histogram match the images before registration.

       -l, --use-estimate-learning-rate-once

              turn  on  the  option  that lets you estimate the learning rate step size only at the beginning of
              each level. * useful as a second stage of fine-scale registration.

       -w, --winsorize-image-intensities [lowerQuantile,upperQuantile]

              Winsorize data based on specified quantiles.

       -x, --masks [fixedImageMask,movingImageMask]

              Image masks to  limit  voxels  considered  by  the  metric.  Two  options  are  allowed  for  mask
              specification: 1) Either the user specifies a single mask to be used for all stages or 2) the user
              specifies a mask for each stage. With the latter one can select to which stages masks are  applied
              by  supplying  valid  file  names.   If  the file does not exist, a mask will not be used for that
              stage. Note that we handle the fixed and moving masks separately to enforce this constraint.

       --float

              Use 'float' instead of 'double' for computations.  <VALUES>: 0

       --minc

              Use MINC file formats for transformations.  <VALUES>: 0

       -v, --verbose (0)/1

              Verbose output.

       -h

              Print the help menu (short version).

       --help

              Print the help menu. Will also print values used on the current command line call.  <VALUES>: 1