antsusedeformationfieldtogetaffinetransform(1) [debian man page]

ANTSUSEDEFORMATIONFIELDTOGETAFFINETRANSFORM(1)			   User Commands		    ANTSUSEDEFORMATIONFIELDTOGETAFFINETRANSFORM(1)

NAME

       ANTSUseDeformationFieldToGetAffineTransform - part of ANTS registration suite

SYNOPSIS

       ANTSUseDeformationFieldToGetAffineTransform zzzWarp.nii.gz load_ratio(ex: 0.01) [rigid | affine] OutAffine.txt [mask.nii.gz]

DESCRIPTION

	      we expect the input deformation field in the same physical space as the images you want to

       load_ratio: ratio of points to be loaded from deformation field (to save memory)

	      the mask gives the region from which points will be selected ...

ANTSUseDeformationFieldToGetAffineTransform 1.9 		     May 2012			    ANTSUSEDEFORMATIONFIELDTOGETAFFINETRANSFORM(1)

IMAGEMATH(1)							   User Commands						      IMAGEMATH(1)

NAME

       ImageMath - part of ANTS registration suite

DESCRIPTION

       Usage: ./ImageMath ImageDimension  OutputImage.ext   Operator   Image1.ext   Image2.extOrFloat

	      some options output text files

	      The last two arguments can be an image or float value Valid Operators : m (multiply)  ,

       +      (add)  ,

       - (subtract)
	      ,

       / (divide)
	      ,

       ^ (power)
	      ,

	      exp  --  take  exponent exp(imagevalue*value) addtozero overadd abs total -- sums up values in an image or in image1*image2 (img2 is
	      the probability mask) Decision -- computes  result=1./(1.+exp(-1.0*( pix1-0.25)/pix2))

	      Neg (Produce Image Negative ) , G Image1.ext s  (Smooth with Gaussian of sigma = s )

       MD Image1.ext
	      s ( Morphological Dilation with radius s ) ,

	      ME Image1.ext s ( Morphological Erosion with radius s ) ,

	      MO Image1.ext s ( Morphological Opening with radius s )

	      MC Image1.ext ( Morphological Closing with radius s )

       GD Image1.ext
	      s ( Grayscale Dilation with radius s ) ,

	      GE Image1.ext s ( Grayscale Erosion with radius s ) ,

	      GO Image1.ext s ( Grayscale Opening with radius s )

	      GC Image1.ext ( Grayscale Closing with radius s )

	      D (DistanceTransform) ,

       Segment Image1.ext N-Classes LocalityVsGlobalityWeight-In-ZeroToOneRange
	      OptionalPriorImages  ( Segment an Image  with option of Priors ,	weight 1 => maximally local/prior-based )

	      Grad Image.ext S ( Gradient magnitude with sigma s -- if normalize, then output in range [0, 1] ) ,

       Laplacian Image.ext S normalize? ( laplacian computed with sigma s --
	      if normalize, then output in range [0, 1] ) ,

	      Normalize image.ext opt ( Normalize to [0,1] option instead divides by average value )

	      PH (Print Header) ,

	      Byte ( Convert to Byte image in [0,255] )

	      LabelStats labelimage.ext valueimage.nii ( compute volumes / masses of objects in a label image -- write to text file )

       ROIStatistics
	      LabelNames.txt labelimage.ext valueimage.nii  ( see the code )

       DiceAndMinDistSum
	      LabelImage1.ext LabelImage2.ext OptionalDistImage  -- outputs DiceAndMinDistSum and Dice Overlap to text log file  +  optional  dis-
	      tance image

       Lipschitz
	      VectorFieldName  -- prints to cout  & writes to image

       InvId VectorFieldName
	      VectorFieldName	-- prints to cout  & writes to image

       GetLargestComponent InputImage {MinObjectSize}
	      -- get largest object in image

       ThresholdAtMean
	      Image  %ofMean

       FlattenImage
	      Image  %ofMax -- replaces values greater than %ofMax*Max to the value %ofMax*Max

	      stack Image1.nii.gz Image2.nii.gz --- will put these 2 images in the same volume CorruptImage Image  NoiseLevel Smoothing TileImages
	      NumColumns  ImageList* RemoveLabelInterfaces ImageIn EnumerateLabelInterfaces ImageIn  ColoredImageOutname  NeighborFractionToIgnore
	      FitSphere  GM-ImageIn  {WM-Image}  {MaxRad-Default=5}  HistogramMatch  SourceImage  ReferenceImage {NumberBins-Default=255} {Number-
	      Points-Default=64} PadImage ImageIn Pad-Number ( if Pad-Number is negative, de-Padding occurs ) Where Image  ValueToLookFor  maskIm-
	      age-option  tolerance --- the where function from IDL TensorFA DTImage TensorColor DTImage --- produces RGB values identifying prin-
	      cipal directions TensorToVector DTImage WhichVec --- produces vector field identifying one of the principal directions, 2 =  largest
	      eigenvalue  TensorToVectorComponent  DTImage WhichVec --- 0 => 2 produces component of the principal vector field , i.e. largest ei-
	      genvalue.   3 = 8 => gets values from the tensor TensorIOTest DTImage --- will write the DT image back out ... tests  I/O  processes
	      for  consistency.   MakeImage   SizeX   SizeY  {SizeZ} SetOrGetPixel  ImageIn Get/Set-Value  IndexX  IndexY {IndexZ}  -- for example
	      ImageMath 2 outimage.nii SetOrGetPixel Image  Get 24 34 -- gets the value at 24, 34

       ImageMath 2 outimage.nii SetOrGetPixel Image 1.e9
	      24 34  -- this sets 1.e9 as the value at 23 34

	      you can also pass a boolean at the end to force the physical space to be used

	      TensorMeanDiffusion DTImage CompareHeadersAndImages Image1 Image2 --- tries to find and fix header error!  output  is  the  repaired
	      image  with new header.  never use this if you trust your header information.  CountVoxelDifference Image1 Image2 Mask --- the where
	      function from IDL stack image1 image2  --- stack image2 onto image1 CorrelationUpdate Image1 Image2  RegionRadius ---  in  voxels  ,
	      Compute  update that makes Image2  more like Image1 ConvertImageToFile  imagevalues.nii {Optional-ImageMask.nii} -- will write voxel
	      values to a file PValueImage  TValueImage  dof ConvertToGaussian	 TValueImage   sigma-float  ConvertImageSetToMatrix   rowcoloption
	      Mask.nii	 *images.nii  --   each row/column contains image content extracted from mask applied to images in *img.nii ConvertVector-
	      ToImage	Mask.nii vector.nii  -- the vector contains image content extracted from a mask - here we return the vector to its spatial
	      origins  as  image content TriPlanarView	ImageIn.nii.gz PercentageToClampLowIntensity  PercentageToClampHiIntensity x-slice y-slice
	      z-slice TruncateImageIntensity inputImage  {lowerQuantile=0.05} {upperQuantile=0.95}   {numberOfBins=65}	 {binary-maskImage}  Fill-
	      Holes  Image  parameter  :  parameter = ratio of edge at object to edge at background = 1 is a definite hole bounded by object only,
	      0.99 is close -- default of parameter > 1 will fill all holes

       PropagateLabelsThroughMask
	      speed/binaryimagemask.nii.gz   initiallabelimage.nii.gz Optional-Stopping-Value  -- final output is the propagated label image

	      optional stopping value -- higher values allow  more  distant  propagation  FastMarchingSegmentation    speed/binaryimagemask.nii.gz
	      initiallabelimage.nii.gz	Optional-Stopping-Value   --  final output is the propagated label image optional stopping value -- higher
	      values allow more distant propagation ExtractSlice  volume.nii.gz slicetoextract --- will extract slice number from  last  dimension
	      of  volume  (2,3,4)  dimensions  ConvertLandmarkFile   InFile.txt ---- will convert landmark file between formats.  see ants.pdf for
	      description of formats.  e.g. ImageMath 3  outfile.vtk  ConvertLandmarkFile  infile.txt

ImageMath 1.9							     May 2012							      IMAGEMATH(1)