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