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)