WARPIMAGEMULTITRANSFORM(1) User Commands WARPIMAGEMULTITRANSFORM(1)NAME
WarpImageMultiTransform - part of ANTS registration suite
DESCRIPTION
Usage:
./WarpImageMultiTransform ImageDimension moving_image output_image -R reference_image --use-NN SeriesOfTransformations--(See Below)
SeriesOfTransformations --- ./WarpImageMultiTransform can apply, via concatenation, an unlimited number of transformations to your
data . Thus, SeriesOfTransformations may be an Affine transform followed by a warp another affine and then another warp.
Inverse affine transformations are invoked by calling
-i MyAffine.txt
InverseWarps are invoked by passing the InverseWarp.nii.gz
filename (see below for a note about this).
Example 1: Mapping a warped image into the reference_image domain by applying abcdWarpxvec.nii.gz/abcdWarpyvec.nii.gz/abcd-
Warpzvec.nii.gz and then abcdAffine.txt
./WarpImageMultiTransform 3 moving_image output_image -R reference_image abcdWarp.nii.gz abcdAffine.txt
Example 2: To map the fixed/reference_image warped into the moving_image domain by applying the inversion of abcdAffine.txt and then
abcdInverseWarpxvec.nii.gz/abcdInverseWarpyvec.nii.gz/abcdInverseWarpzvec.nii.gz .
./WarpImageMultiTransform 3 reference_image output_image -R moving_image -i abcdAffine.txt abcdInverseWarp.nii.gz
Note that the inverse maps (Ex. 2) are passed to this program in the reverse order of the forward maps (Ex. 1).
This makes sense, geometrically ... see ANTS.pdf for visualization of this syntax.
Compulsory arguments:
ImageDimension: 2 or 3 (for 2 or 3 Dimensional registration)
moving_image: the image to apply the transformation to
output_image: the resulting image
Optional arguments:
-R: reference_image space that you wish to warp INTO.
--tightest-bounding-box: Computes the tightest bounding box using all the affine transformations. It will be overrided by -R refer-
ence_image if given. --reslice-by-header: equivalient to -i -mh, or -fh -i -mh if used together with -R. It uses the orientation
matrix and origin encoded in the image file header. It can be used together with -R. This is typically not used together with any
other transforms.
--use-NN: Use Nearest Neighbor Interpolation.
--use-BSpline: Use 3rd order B-Spline Interpolation.
-i: will use the inversion of the following affine transform.
Other Example Usages: Reslice the image: WarpImageMultiTransform 3 Imov.nii.gz Iout.nii.gz --tightest-bounding-box
--reslice-by-header Reslice the image to a reference image: WarpImageMultiTransform 3 Imov.nii.gz Iout.nii.gz -R Iref.nii.gz
--tightest-bounding-box --reslice-by-header
Important Notes: Prefixname "abcd" without any extension will use ".nii.gz" by default The abcdWarp and abcdInverseWarp do not
exist. They are formed on the basis of abcd(Inverse)Warpxvec/yvec/zvec.nii.gz when calling ./WarpImageMultiTransform, yet you have
to use them as if they exist.
WarpImageMultiTransform 1.9 May 2012 WARPIMAGEMULTITRANSFORM(1)
Check Out this Related Man Page
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)