Provided by: ants_1.9.2+svn680.dfsg-4_amd64 
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 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 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