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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 (img2 is the 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 labelimage.ext valueimage.nii ( see the code )

       DiceAndMinDistSum
              LabelImage1.ext LabelImage2.ext  OptionalDistImage   --  outputs
              DiceAndMinDistSum  and  Dice Overlap to text log file + optional
              distance 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}    {NumberPoints-Default=64}   PadImage
              ImageIn Pad-Number  (  if  Pad-Number  is  negative,  de-Padding
              occurs  )  Where Image ValueToLookFor maskImage-option tolerance
              --- the where function from  IDL  TensorFA  DTImage  TensorColor
              DTImage --- produces RGB values identifying principal 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
              eigenvalue.   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  ConvertVectorToImage
              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} FillHoles 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