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)