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