NAME

       antsSliceRegularizedRegistration - part of ANTS registration suite

DESCRIPTION

   COMMAND:
              antsSliceRegularizedRegistration

              antsSliceRegularizedRegistration  This  program  is  a  user-level  application for slice-by-slice
              translation registration. Results are regularized in z using polynomial regression. The program is
              targeted at spinal cord MRI. Only one stage is supported where a stage consists of a transform; an
              image metric; and iterations, shrink factors, and smoothing sigmas for each level. Specialized for
              3D data: fixed image is 3D, moving image is 3D.  Registration  is  performed  slice-by-slice  then
              regularized   in   z.   The   parameter   -p  controls  the  polynomial  degree.  -p  0  means  no
              regularization.Implemented by B. Avants and conceived by Julien Cohen-Adad.

       Outputs:

              OutputPrefixTxTy_poly.csv: polynomial fit to Tx &

              Ty

              OutputPrefix.nii.gz: transformed image

       Example call:

              antsSliceRegularizedRegistration  -p  4  --output  [OutputPrefix,OutputPrefix.nii.gz]  --transform
              Translation[0.1]  --metric MI[ fixed.nii.gz, moving.nii.gz , 1 , 16 , Regular , 0.2 ] --iterations
              20 --shrinkFactors 1 --smoothingSigmas 0

   OPTIONS:

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

              MI[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={Regular,Random,None}>,<samplingPercentage=[0,1]>]
              MeanSquares[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random,None}>,<samplingPercentage=[0,1]>]
              GC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random,None}>,<samplingPercentage=[0,1]>]

              Four  image  metrics  are  available---  GC  :  global  correlation,  CC:  ANTS neighborhood cross
              correlation, MI: Mutual information, and MeanSquares: mean-squares intensity difference. Note that
              the metricWeight is currently not used. Rather, it is a temporary place holder until  multivariate
              metrics are available for a single stage.

       -x, --mask mask-in-fixed-image-space.nii.gz

              Fixed image mask to limit voxels considered by the metric.

       -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.

       -t, --transform Translation[gradientStep]
              Rigid[gradientStep] Similarity[gradientStep]

              Several transform  options  are  available.  The  gradientStep  orlearningRate  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.

       -i, --iterations MxNx0...

              Specify the number of iterations at each level.

       -s, --smoothingSigmas MxNx0...

              Specify the amount of smoothing at each level.

       -f, --shrinkFactors MxNx0...

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

       -o, --output [outputTransformPrefix,<outputWarpedImage>,<outputAverageImage>]

              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.

       -h, --help

              Print the help menu (short version).  <VALUES>: 1, 0

       -v, --verbose

              verbose option <VALUES>: 0

       -p, --polydegree

              degree  of  polynomial  -  up  to  zDimension-2.  Controls  the  polynomial  degree.  0  means  no
              regularization.  This may be a vector denoted by 2x2x1 for a 3-parameter transform ( e.g. rigid ).
              This would regularize the translation by 2nd degree  polynomial  and  the  rotation  by  a  linear
              function.

antsSliceRegularizedRegistration 2.5.4+dfsg       February 2025              ANTSSLICEREGULARIZEDREGISTRATION(1)