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This page contains additional information on how to use clitk tools:

clitk4DImageToNVectorImage

clitk4DImageToNVectorImage 1.0

Convert the 4th dimension of a 4D Image into a VectorPixel 3D Image

Usage: clitk4DImageToNVectorImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename

clitkAffineRegistration

clitk 1.0

Perform an affine registration between two images.

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
<style="" & quot;text-align:center& quot; "">Run Time:
-v --verbose Verbose (default=off)
--gradient If verbose, show gradient at each iteration (default=off)
--threads=INT Number of threads to use (default=min(#cores,8))
<style="" & quot;text-align:center& quot; "">Input (Both images have to be of the same dimension (2 or 3D). For 2D-3D
<style="" & quot;text-align:center& quot; "">(non-projective) registrations, give the 2D image a third dimension of 1 and
<style="" & quot;text-align:center& quot; "">set it to the reference image.):
-i --reference=STRING Reference or fixed image filename
-j --target=STRING Target or moving image filename
-m --referenceMask=STRING Mask to placed over the reference image
--targetMask=STRING Mask to placed over the target image
<style="" & quot;text-align:center& quot; "">Output:
-o --output=STRING Transformed object image filename
--checker_after=STRING Checherboard representation of the transformed object image and reference image
--checker_before=STRING Checherboard representation of the object image and reference image
--after=STRING Difference between the reference image and the transformed object
--before=STRING Difference between the reference image and the original object image
--matrix=STRING Affine matrix (reference to object space) filename
<style="" & quot;text-align:center& quot; "">Interpolator:
--interp=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpSF=INT Sampling factor if BLUT (default=`20')
<style="" & quot;text-align:center& quot; "">Transform (Input and Output transformation parameters map the physical space
<style="" & quot;text-align:center& quot; "">of the fixed or reference image into the physical space of the moving or object
<style="" & quot;text-align:center& quot; "">image. Positive rotations result in a counter-clockwise rotation for the moving
<style="" & quot;text-align:center& quot; "">image. Positive translations result in shift along the negative axis for the
<style="" & quot;text-align:center& quot; "">moving image.):
--transform=INT Type: 0=Identity, 1=Translation, 2=Rigid, 3=Affine (default=`2')
-x --transX=FLOAT 1-3: Initial translation in mm along the X axis (default=`0.0')
-y --transY=FLOAT 1-3: Initial translation in mm along the Y axis (default=`0.0')
-z --transZ=FLOAT 1-3: Initial translation in mm along the Z axis (default=`0.0')
--initMatrix=STRING 1-3: Initial matrix (reference to object space) filename
--moment 1-3: Initialize translation by aligning the center of gravities for the respective intensities (default=off)
<style="" & quot;text-align:center& quot; "">Metric (optimized, threaded versions are available for *, compile ITK with
<style="" & quot;text-align:center& quot; "">REVIEW and OPT_REGISTRATION enabled):
--metric=INT Type: 0=Mean-Squares*, 1=Normalized CC*, 2=Histogram CC, 3=Gradient-Difference, 4=Viola-Wells MI, 5=Histogram MI, 6=Mattes' MI*, 7=Normalized MI, 8=CR, 9=SSD for BLUT FFD** (default=`0')
--samples=FLOAT Specify fraction [0, 1] of samples of the reference image used for the metric (* only). Use high fraction for detailed images (eg. 0.2, 0.5), for smooth images 0.01 might be enough. (default=`1')
--intThreshold=FLOAT Fixed image samples intensity threshold (* only; caution with --normalize)
--subtractMean 1: Subtract mean for NCC calculation (narrows optimal) (default=on)
--bins=INT 2,5-8: Number of histogram bins (default=`50')
--random 4,6: Samples should be taken randomly, otherwise uniformly (default=off)
--stdDev=FLOAT 4: specify the standard deviation in mm of the gaussian kernels for both PDF estimations (default=`0.4')
--explicitPDFDerivatives 6: Calculate PDF derivatives explicitly (affine=true; FFD=false) (default=on)
<style="" & quot;text-align:center& quot; "">Preprocessing:
--normalize Normalize images before registration (not necessary for metric 1,2,5,6,8; caution with
--intThreshold) (default=off)
--blur=FLOAT Blur images before registration, use Gaussian with std dev (none by default) (default=`0.0')
<style="" & quot;text-align:center& quot; "">Optimizer:
--optimizer=INT 0=Simplex, 1=Powell, 2=FRPR, 3=Regular Step GD, 4=VersorRigid3D, 5=Conjugated Gradient, 6=L-BFGS, 7=L-BFGS-B (default=`0')
--delta=DOUBLE 0: Initial delta, otherwise automatic
--step=DOUBLE 1,2,3,4: Initial stepsize (to be multiplied with the gradient) (default=`2.0')
--relax=DOUBLE 3,4: Relaxation of the stepsize (multiplied each time the gradient changes sign) (default=`0.7')
--valueTol=DOUBLE 0,1,2: Tolerance on the function (default=`0.01')
--stepTol=DOUBLE 0,1,3,4: Tolerance on the step size (default=`0.1')
--gradTol=DOUBLE 3,4,6,7: Tolerance on the (projected) gradient magnitude (7: 1=low->1e-10=high precision) (default=`1e-5')
--lineAcc=DOUBLE 6: Line accuracy (eg: high=0.1, low=0.9) (default=`0.9')
--convFactor=DOUBLE 7: Convergence factor: terminate if factor*machine_precision>reduction in cost (1e+12 low, 1e+7 moderate and 1e+1 high precision) (default=`1e+12')
--maxIt=INT 0-7: Maximum number of iterations (default=`500')
--maxLineIt=INT Maximum number of line iterations (default=`50')
--maxEval=INT Maximum number of evaluations (default=`500')
--maxCorr=INT Maximum number of corrections (default=`5')
--selectBound=INT 7: Select the type of bound: 0=none, 1=u, 2=u&l, 3=l (default=`0')
--lowerBound=DOUBLE 7: The lower bound
--upperBound=DOUBLE 7: The upper bound
--rWeight=FLOAT Weight of 1° of rotation during optimisation (high weight, less change) (default=`50.0')
--tWeight=FLOAT Weight of 1mm of translation during optimisation (high weight, less change) (default=`1.0')
--levels=INT Number of resolution levels (default=`1')
--inc=FLOAT Increment factor (x) previous step/tol = new step/tol at next resolution level (default=`1.2')
--dec=FLOAT Decrement factor (:) previous step/tol = new step/tol at next resolution level (default=`4')

clitkAffineTransform

clitkAffineTransform 1.0

Resample with or without affine transform of 2D, 3D, 4D images or vector fields

Usage: clitkAffineTransform [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-l --like=STRING Resample output this image (size, spacing, origin, direction)
--transform_grid Apply affine transform to input grid for output's (default=off)
<style="" & quot;text-align:center& quot; "">Options:
--size=INT New output size if different from input
--spacing=DOUBLE New output spacing if different from input
--spacinglike=STRING New output spacing like this image
--origin=DOUBLE New output origin if different from input
--direction=DOUBLE New output direction if different from input
-m --matrix=STRING Affine matrix (homogene) filename
-e --elastix=STRING Read EulerTransform from elastix output file (combine if multiple)
-r --rotate=DOUBLE Rotation to apply (radians)
-t --translate=DOUBLE Translation to apply (mm)
--pad=DOUBLE Edge padding value (default=`0.0')
--adaptive Adapt the size, spacing or the origin when one of the previous tag is on (use previous clitkResampleImage) (default=off)
<style="" & quot;text-align:center& quot; "">Interpolation:
--interp=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpSF=INT Sampling factor if BLUT (default=`20')
--interpVF=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpVFOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpVFSF=INT Sampling factor if BLUT (default=`20')
<style="" & quot;text-align:center& quot; "">Gaussian filtering:
-g --gauss=DOUBLE Apply gaussian filter before (sigma in mm) (default=0.0)
--autogauss Apply gaussian filter before with auto sigma when downsampling (default=off) (default=off)

clitkAnisotropicDiffusion

clitkAnisotropicDiffusion 1.0

Performs gradient or curvature anisotropic diffusion filtering

Usage: clitkAnisotropicDiffusion [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
--type=ENUM Type of filtering (possible values="Gradient", "Curvature" default=`Gradient')
-n --niterations=INT Number of iterations (default=`5')
-c --conductance=DOUBLE Conductance (default=`3')
-t --timestep=DOUBLE Time step (default=`0.01')

clitkAutoCrop

clitkAutoCrop 1.0

Crop a mask image

Usage: clitkAutoCrop [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
--imagetypes Display allowed image types (default=off)
-v --verbose Verbose (default=off)
--verboseOption Display options values (default=off)
--verboseWarningOff Do not display warning (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
--BG=DOUBLE Background value in input. (default=`0')

clitkBackProjectImage

clitk Back project a 2D image with cone-beam geometry

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
<style="" & quot;text-align:center& quot; "">Run Time:
-v --verbose Verbose (default=off)
--threads=INT Number of threads to use (default=min(cores,8))
<style="" & quot;text-align:center& quot; "">Input:
-i --input=STRING Input grid filename
-o --output=STRING Output grid filename
-m --mask=STRING 3D Mask in which the filter should be applied (not supported yet;-)
<style="" & quot;text-align:center& quot; "">Projection Parameters:
--iso=FLOAT The isocenter (default=`0.0')
--screen=FLOAT Specify the source to screen distance in mm (default=`1536.0')
--axis=FLOAT Specify the source to axis distance in mm (default=`1000.0')
--angle=FLOAT Specify the projection angle (default=`0.0')
--matrix=STRING Rigid tranform prior to projection (4x4)
--pad=FLOAT Padding value (default=`0.0')
--panel_shift=DOUBLE Precise position of the panel in mm
<style="" & quot;text-align:center& quot; "">Output Image:
--like=STRING Make output like this image
--origin=DOUBLE Origin for the output image (default=`0.0')
--size=INT Size for the output image (default=`100')
--spacing=DOUBLE Spacing for the output image (default=`1.0')

clitkBinarizeImage

clitkBinarizeImage 1.0

Usage: clitkBinarizeImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-l --lower=DOUBLE Lower intensity (default=min), fg is greater than this value
-u --upper=DOUBLE Upper intensity (default=max), fg is lower than this value
--fg=DOUBLE Foreground (FG) or 'inside' value (default=`1')
--bg=DOUBLE Background (BG) or 'ouside' value (default=`0')
--mode=STRING Use FG and/or BG values (if FG, the BG is replaced by the input image values) (possible values="FG", "BG", "both" default=`both')
-p --percentage=DOUBLE Percentage of total pixels values (in %)

clitkBlurImage

clitkBlurImage 1.0

Filter the input image with a Gaussian

Usage: clitkBlurImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
--variance=DOUBLE value of the gaussian variance (multiple values=number of image dimension) in mm² - default=1.0

clitkBLUTDIR

clitk Register 2 images using optimized BLUT FFD...

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
<style="" & quot;text-align:center& quot; "">Run Time:
-v --verbose Verbose (default=off)
--threads=INT Number of threads to use (default=min(#cores,8))
<style="" & quot;text-align:center& quot; "">Input:
-r --reference=STRING Input reference 3D image (float)
-t --target=STRING Input target 2D image (float)
-m --referenceMask=STRING Mask or labels to placed over the reference image
--targetMask=STRING Mask to placed over the target image
<style="" & quot;text-align:center& quot; "">Output:
--vf=STRING Result DVF
--coeff=STRING Result coefficient images
--coeffEveryN=INT Result coefficient images at every N iterations (requires --coeff and --verbose) (default=`20')
-o --output=STRING Deformed target image
--before=STRING Difference image before (but after rigid transform)
--after=STRING Difference image after
<style="" & quot;text-align:center& quot; "">Transform (Note that only one of --control, --spacing is required. The other
<style="" & quot;text-align:center& quot; "">will be adjusted to fit the region and allow exact representation.
<style="" & quot;text-align:center& quot; "">SamplingFactor will be set accordingly:
--initMatrix=STRING Prior rigid/affine transform matrix from reference to target space
--centre Centre images before starting registration (ignored if initMatrix was given) (default=off)
--initCoeff=STRING Initial coefficient image
--order=INT Spline Order FFD (default=`3')
--control=INT Internal control points for each dimension
--spacing=DOUBLE Control point spacing for each dimension (mm)
--samplingFactor=INT LUT sampling factor
--itkbspline Use ITK BSpline instead of multilabel BLUT for debug (default=off)
<style="" & quot;text-align:center& quot; "">Interpolator:
--interp=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpSF=INT Sampling factor if BLUT (default=`20')
<style="" & quot;text-align:center& quot; "">Metric (optimized, threaded versions are available for *, compile ITK with
<style="" & quot;text-align:center& quot; "">REVIEW and OPT_REGISTRATION enabled. Further optimized versions ** for BLUT
<style="" & quot;text-align:center& quot; "">FFD optimizing a !3D! vector field):
--metric=INT Type: 0=SSD*, 1=Normalized CC*, 2=Histogram CC, 3=Gradient-Difference, 4=Viola-Wells MI, 5=Histogram MI, 6=Mattes' MI*, 7=Normalized MI, 8=CR, 9=SSD for BLUT FFD**, 10=CC for BLUT FFD**, 11=Mattes' MI for BLUT FFD** (default=`0')
--samples=FLOAT Specify fraction [0, 1] of samples of the reference image used for the metric (* only). Use high fraction for detailed images (eg. 0.2, 0.5), for smooth images 0.01 might be enough. (default=`1')
--intThreshold=FLOAT Fixed image samples intensity threshold (* only)
--subtractMean 1: Subtract mean for NCC calculation (narrows optimal) (default=on)
--bins=INT 2,5-8: Number of histogram bins (default=`50')
--random 4,6: Samples should be taken randomly, otherwise uniformly (default=off)
--stdDev=FLOAT 4: specify the standard deviation in mm of the gaussian kernels for both PDF estimations (default=`0.4')
--explicitPDFDerivatives 6: Calculate PDF derivatives explicitly (rigid=true; FFD=false) (default=off)
<style="" & quot;text-align:center& quot; "">Optimizer:
--optimizer=INT 0=Simplex, 1=Powell, 2=FRPR, 3=Regular Step GD, 4=VersorRigid3D, 5=Conjugated Gradient, 6=L-BFGS, 7=L-BFGS-B (default=`7')
--delta=DOUBLE 0: Initial delta, otherwise automatic
--step=DOUBLE 1,2,3,4: Initial stepsize (to be multiplied with the gradient) (default=`2.0')
--relax=DOUBLE 3,4: Relaxation of the stepsize (multiplied each time the gradient changes sign) (default=`0.7')
--valueTol=DOUBLE 0,1,2: Tolerance on the function (default=`0.01')
--stepTol=DOUBLE 0,1,3,4: Tolerance on the step size (default=`0.1')
--gradTol=DOUBLE 3,4,6,7: Tolerance on the (projected) gradient magnitude (7: 1=low->1e-10=high precision) (default=`1e-5')
--lineAcc=DOUBLE 6: Line accuracy (eg: high=0.1, low=0.9) (default=`0.9')
--convFactor=DOUBLE 7: Convergence factor: terminate if factor*machine_precision>reduction in cost (1e+12 low -> 1e+1 high precision) (default=`1e+7')
--maxIt=INT 0-7: Maximum number of iterations (default=`500')
--maxLineIt=INT 1,2: Maximum number of line iterations (default=`50')
--maxEval=INT 6,7: Maximum number of evaluations (default=`500')
--maxCorr=INT 7: Maximum number of corrections (default=`5')
--selectBound=INT 7: Select the type of bound: 0=none, 1=u, 2=u&l, 3=l (default=`0')
--lowerBound=DOUBLE 7: The lower bound (default=`0.0')
--upperBound=DOUBLE 7: The upper bound (default=`0.0')
<style="" & quot;text-align:center& quot; "">Registration:
--levels=INT Number of resolution levels (default=`1')
--skipLastPyramidLevel Skip full resolution pyramid level (default=off)
--intermediate=STRING Write the coefficient image of the intermediate levels (provide levels filenames)

clitkCalculateTRE

clitkCalculateTRE 1.0

Calculate TRE: give a reference point list and 1 or more target point lists. In case of the latter, the number of DVF (or the size of the 4th D) given should match the number of lists. Use --shipFirst to skip the first phase of a 4D DVF. General summarizes for all points (mean, SD, max) in magnitude and par component. Tre and warp gives all values for all points.

Usage: clitkCalculateTRE [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">Input:
--ref=STRING List of points in reference
-i --input=STRING Lists of points in targets
--vf=STRING Input deformation fields
--coeff=STRING Input coefficient images
--skip=INT Skip a phase of a 4D DVF
<style="" & quot;text-align:center& quot; "">Interpolation:
--interpVF=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpVFOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpVFSF=INT Sampling factor if BLUT (default=`20')
<style="" & quot;text-align:center& quot; "">Output:
--general=STRING Summarized TRE values (mean, SD, max)
--original=STRING Original distances: base filename
--originalMag=STRING Original magnitude of distances: base filename
--displacement=STRING Estmated displacements: base filename
--displacementMag=STRING Estimated magnitude displacements: base filename
--tre=STRING All TRE values: base filename
--treMag=STRING All TRE magnitude values: base filename
--warp=STRING All warped points: base filename

clitkCatImage

clitkCatImage 1.0

Concatenate two images along chosen direction

Usage: clitkCatImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input1=STRING First input image filename
-j --input2=STRING Second input image filename
-o --output=STRING Output image filename
-d --dimension=INT Dimension on which to concatenate

clitkChangeDicomTag

clitkChangeDicomTag 1.0

Usage: clitkChangeDicomTag [OPTIONS]... [FILES]...

Change Dicom tag -k value to -t
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input dicom file
-o --output=STRING Output dicom file
-k --key=STRING Keys of tags to modify (default=`0008
-t --tag=STRING Tags values (default=`MIDPOSITION')

clitkChangeImageInfo

clitkChangeImageInfo 1.0

Change the information (spacing, origin, direction...) of an image

Usage: clitkChangeImageInfo [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-s --spacing=DOUBLE Spacing
--origin=DOUBLE Origin
-d --direction=DOUBLE Direction

clitkComposeVF

clitk Read two vector fields (.mhd, .vf, ..) and compose them using linear interpolation

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input1=STRING Input1 VF filename
-j --input2=STRING Input2 VF filename
-o --output=STRING Output VF filename
-t --type=INT Type of input images (0: DVF, 1: b-spline coefficient images) (default=`0')
-l --like=STRING Image to read output parameters from (obligatory if type=1)
-p --pad=FLOAT Edgepadding value (default=`0.0')
-v --verbose Verbose (default=off)

clitkConnectedComponentLabeling

clitkConnectedComponentLabeling 1.0

Basic segmentation : connected component labeling

Usage: clitkConnectedComponentLabeling [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
--verboseOption Display options values (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
--inputBG=INT Input Background (default=`0')
-o --output=STRING Output filename
<style="" & quot;text-align:center& quot; "">Labelize:
--minSize=INT Minimum component size in voxels (default=`100')
--full Full connecticity (default=off)

clitkConvertBSplineDeformableTransformToVF

clitkConvertBSplineDeformableTransformToVF 1.0

Convert a BSpline transform to a DVF with given properties

Usage: clitkConvertBSplineDeformableTransformToVF [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">IO:
-i --input=STRING Input BLUT-coefficient image filename
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Output Image Properties:
--like=STRING Make output like this image
--origin=DOUBLE Origin for the output image (default=`0.0')
--size=INT Size for the output image (default=`100')
--spacing=DOUBLE Spacing for the output image (default=`1.0')
<style="" & quot;text-align:center& quot; "">Transform:
-t --type=INT Type (0: itk bspline; 1: BLUT) (default=`0')
--order=INT 1: Spline order
--mask=STRING 1: Mask image filename
--shape=INT 1: Transform shape: 0=egg, 1=diamond (default=`0')

clitkCropImage

clitkCropImage 1.0

Crop an image according to a given extends or AutoCrop with a background value or like another image. In all cases, by default, the output origin is set to be able to overlay input and output without registration.

Usage: clitkCropImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
--imagetypes Display allowed image types (default=off)
-v --verbose Verbose (default=off)
--verboseOption Display options values (default=off)
--verboseWarningOff Do not display warning (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Used determined crop:
-b --boundingBox=INT Bounding box of the crop region in pixel (in 3D: =x1,x2,y1,y2,z1,z2)
-l --lower=INT Size of the lower crop region (multiple values)
-u --upper=INT Size of the upper crop region (multiple values)
--origin Set new origin to zero (default=off)
<style="" & quot;text-align:center& quot; "">AutoCrop with BG value:
--BG=DOUBLE Background value in input. (default=`0')
<style="" & quot;text-align:center& quot; "">Crop like another image:
--like=STRING Crop like this image (must have the same spacing
--updateOrigin By default, with like image, the output origin is the same than the like image. Set to on the flag to keep the origin. (default=off)
--BGLike=DOUBLE Background value in output (if like larger) (default=`0')

clitkDecomposeAndReconstruct

clitkDecomposeAndReconstruct 1.0

Decompose through erosion, and reconstruct through dilation. Erode a binary image to decompose into different labels, keeping a record of the eroded regions (=erosion padding value). Dilate all labels of a label image
separately, only dilating the marked regions (erosion padding value).

Usage: clitkDecomposeAndReconstruct [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Parameters:
-t --type=INT 0=Erode to decompose(binary image) , 1=Dilate to reconstuct(label image) , 2= 1(0(x)) (default=`0')
-f --full Use full connectivity (1 side connected enough) (default=on)
--fg=FLOAT 0: Foreground value (erode only this label)
--bg=FLOAT 1: Background value (ignore this label) (default=`0')
--pad=FLOAT 0,1: The erosion padding value (default=`-1')
-b --bound 0-1: Set borders to foreground (default=off)
-r --radius=INT Use binary ball element with given radius (default=`1')
-n --new=INT 0,2: Erode till at least n new labels appear (default=`1')
--max=INT 1,2: Consider only the n largest labels (rest will be put to fg) (default=`10')
--min=INT 0,2: Minimum number of erosions (default=`1')
--minSize=INT 0,2: Minimum object size (default=`10')

clitkDemonsDeformableRegistration

clitk Apply Demons registration between (2D or 3D) images...

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
<style="" & quot;text-align:center& quot; "">Run Time:
-v --verbose Verbose (default=off)
--threads=INT Number of threads to use for intensive algorithms (default=min(cores,8))
--debug Give debug info (default=off)
<style="" & quot;text-align:center& quot; "">Input:
-r --reference=STRING Input reference image
-t --target=STRING Input target image
--init=STRING Input initial deformation field
<style="" & quot;text-align:center& quot; "">Output:
--vf=STRING Result DVF
-o --output=STRING Deformed target image
--before=STRING Difference image before
--after=STRING Difference image after
<style="" & quot;text-align:center& quot; "">Demons:
--demons=INT Type: 0=normal, 1=symm, 2=fast symm, 3=diffeomorphic (default=`3')
--levels=INT Number of resolution levels (default=`1')
--maxIter=INT Maximum number of iterations at each resolution level (default=`50')
--maxRMSError=DOUBLE Maximum RMS error at each resolution level (default=`1')
--stop=INT Maximum oscillations at each resolution level (-1=unset) (default=`-1')
--sd=DOUBLE SD (in mm) for smoothing in each dimension (default=`2.0')
--maxStep=DOUBLE 2,3: Maximum step size (mm) (default=`2')
--scaleSD Scale SD to coarse resolution levels (default=off)
--scaleStep 2,3: Scale maximum step size to coarse resolution levels (default=off)
--fluid Smooth update field instead of deformation field (default=off)
--spacing Use image spacing for derivatives (non-isotropic voxels) (default=off)
--intThreshold=DOUBLE 0,1,2: Intensity threshold to consider intensity equal (default=`0.001')
--movGrad 1: Use moving image gradient (default=off)
--gradType=INT 2,3: 0=Symmetric, 1=fixed, 2=warpedMoving, 3=mappedMoving (default=`0')
--firstOrder 3: Use first order approx for exponential (default=off)

clitkDice

clitkDice 1.0

Compute Dice between labeled images. Background must be 0.

Usage: clitkDice [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
<style="" & quot;text-align:center& quot; "">General options:
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-l --long Long display (not only dice) (default=off)
<style="" & quot;text-align:center& quot; "">Input:
-i --input1=STRING Input mask 1
-j --input2=STRING Input mask 2
--label1=INT Label in input1 (default=`1')
--label2=INT Label in input2 (default=`1')

clitkDicom2Image

clitk Try to convert a DICOM into an image (.hdr, .vox...) identifying all available series

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-t --tolerance=DOUBLE Tolerance for slice position (default=`0')
-o --output=STRING Output image filename
--std_input Take the like of input file from stdin, to support huge lists of filenames (default=off)
--focal_origin Output files with FOCAL-like origin, instead of the origin present in the dicom files (default=off)
-p --patientSystem Open the image with patient coordinate system (default=off)
-n --instanceNumber Sort the images regarding instance number in dicom tag (default=off)
-r --reverse Reverse the slice order (default=off)

clitkDicomInfo

clitk read and print Dicom header

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-s --studyID Only display Study UID (default=off)
-u --uniq Do not display if same study UID (default=off)
-f --filename Display filename (default=off)

clitkDicomRTPlan2Gate

clitk 1.0

Convert DicomRTPlan to Gate compatible file

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING config file
-i --input=STRING Input dicom file name
-o --output=STRING Output text file name
-v --verbose verbose (default=off)

clitkDicomRTStruct2Image

clitk 1.0

Usage: clitk [OPTIONS]... [FILES]...

Convert DICOM RT Structure Set (contours) to binary image
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--verboseFile Verbose file content (default=off)
-i --input=STRING Input Dicom file
-j --image=STRING Used to read image info (spacing, origin)
-o --output=STRING Output image base filename (roi number and extension will be append)Group: ROIoptionan option of this group is required
-r --roi=INT ROI to binarize (if -1 = all roi) (default=`-1')
-n --roiName=STRING ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value) (default=`')
-s --roiNameSubstr=STRING Substring of ROI name to binarize (reuturns all matches; if blank, use given 'roiName' value) (default=`')
-c --crop Crop binary mask (default=off)
--mha Write the RTStruct as a mha image to avoid special character problems (default=off)
--vtk Write the vtk Mesh as a vtk file (default=off)

clitkDicomWave2Text

clitk 1.2

Extract data from a Dicom wave file to a text file

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING config file
-i --InputFile=STRING Dicom inputfile name
-o --OutputFile=STRING Text outputfile name
-v --Verbose=INT verbose

clitkElastixTransformToMatrix

clitkElastixTransformToMatrix 1.0

Usage: clitkElastixTransformToMatrix [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input elastix filename
-o --output=STRING Output matrix filename

clitkExtractBones

clitkExtractBones 1.0

Extract bony anatomy through thresholding and connected component labelling. Resample mask afterwards (interp= NN) to match another one (like)

Usage: clitkExtractBones [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
--imagetypes Display allowed image types (default=off)
-v --verbose Verbose (default=off)
--verboseStep Verbose each step (default=off)
-w --writeStep Write image at each step (default=off)
--verboseOption Display options values (default=off)
--verboseWarningOff Do not display warning (default=off)
--verboseMemory Display memory usage (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-a --afdb=STRING Output Anatomical Feature DB (Carina position)
<style="" & quot;text-align:center& quot; "">Smoothing (curvature anistropic diffusion):
--smooth smooth input image (default=off)
--spacing Use image spacing (default=off)
--cond=DOUBLE Conductance parameter (default=`3.0')
--time=DOUBLE Time step (0.125 for 2D and 0.0625 for 3D) (default=`0.0625')
--iter=DOUBLE Iterations (default=`5')
<style="" & quot;text-align:center& quot; "">Initial connected component labelling (CCL):
--lower1=DOUBLE Lower threshold for CCL (default=`100')
--upper1=DOUBLE Upper threshold for CCL (default=`1500')
--minSize=INT Minimal Component Size for CCL (default=`100')
--full Use full connectivity (one side is enough) (default=off)
<style="" & quot;text-align:center& quot; "">Neighborhood Connected Region Growing (RG):
--lower2=DOUBLE Lower threshold for RG (default=`10')
--upper2=DOUBLE Upper threshold for RG (default=`1500')
--radius2=INT Neighborhood radius (default=`1')
--sampleRate2=INT Sample rate of label image for RG: number of voxels to skip between seeds (default=`0')
<style="" & quot;text-align:center& quot; "">Fill holes:
--doNotFillHoles Do not fill holes if set (default=on)
-d --dir=INT Directions (axes) to perform filling (defaults to 2,1,0)
--noAutoCrop If set : do no crop final mask to BoundingBox (default=off)

clitkExtractLung

clitkExtractLungs 1.0

Segment lungs in CT image. Need 'patient' mask.

Usage: clitkExtractLungs [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
--imagetypes Display allowed image types (default=off)
-v --verbose Verbose (default=off)
--verboseStep Verbose each step (default=off)
-w --writeStep Write image at each step (default=off)
--verboseOption Display options values (default=off)
--verboseWarningOff Do not display warning (default=off)
--verboseMemory Display memory usage (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input CT image filename
-a --afdb=STRING Output Anatomical Feature DB (Carina position) (default=`default.afdb')
-o --output=STRING Output lungs mask filename (default=`lung.mhd')
-t --outputTrachea=STRING Output trachea mask filename (default=`trachea.mhd')
<style="" & quot;text-align:center& quot; "">Step 1 : Air remove:
--lower=INT Initial lower threshold
--upper=INT Initial upper threshold (default=`-300')
--minSize=INT Minimum component size in voxels (default=`100')
<style="" & quot;text-align:center& quot; "">Step 2 : find trachea:
--type=INT trachea finding algorithm (0: original; 1: LOLA11) (default=`0')
--skipslices=INT 0: Number of slices to skip before searching seed (default=`0')
--upperThresholdForTrachea=DOUBLE --upperThresholdForTrachea=DOUBLE0: Initial upper threshold for trachea (default=`-900')
--multiplierForTrachea=DOUBLE --multiplierForTrachea=DOUBLE0: Multiplier for the region growing (default=`5')
--thresholdStepSizeForTrachea=INT --thresholdStepSizeForTrachea=INT0: Threshold step size (default=`64')
--seed=FLOAT 0,1: Index of the trachea seed point (in mm NOT IN PIXELS)
--doNotCheckTracheaVolume 0,1: If set, do not check the trachea volume (default=off)
--verboseRG 0,1: Verbose RegionGrowing (default=off)
--maxElongation=FLOAT 1: Maximum allowed elongation of candidate regions for the trachea (default=`0.5')
--numSlices=INT 1: Number of slices to search for trachea (default=`50')
--seedPreProcessingThreshold=INT --seedPreProcessingThreshold=INT1: Threshold for the pre-processing step of the algorithm (default=`-400')
<style="" & quot;text-align:center& quot; "">Step 3 : auto extract lung:
--bins=INT Number of bins to use for the Otsu thresholding (default=`500')
<style="" & quot;text-align:center& quot; "">Step 4 : remove trachea:
--radius=INT Radius for dilation (default=`1')
<style="" & quot;text-align:center& quot; "">Step 5 : [optional] openclose:
--openclose Perform an OpenClose operation (default=off)
--opencloseRadius=INT OpenClose radius (default=`1')
<style="" & quot;text-align:center& quot; "">Step 6 : fill holes:
--doNotFillHoles Do not fill holes if set (default=on)
<style="" & quot;text-align:center& quot; "">Step 7 : lung separation (labelling):
--doNotSeparateLungs Do not separate lungs if set (default=off)
--removeSmallLabel Remove small label (stomach?) before separation (default=on)
--noAutoCrop If set : do no crop final mask to BoundingBox (default=off)

clitkExtractPatient

clitkExtractPatient 1.0

Input is binarized using initial thresholds, connected components are labeled (firstLabel). The air label (1) is removed. The remaining is binarized and relabeled, patient should now be the principal label (secondLabel). Two mechanismes are provided to influence the label images. Crop to reduce connectivity (image is restored to original size), eg for SBF. Decomposition through erosion and reconstruction through dilation (slow), eg for Pulmo bellows. Choose which labels to keep from second Label image. Final mask is cleaned by opening and closing. The image is padded first with air. If lungs are touching the border (so the air), set openingRadius to 1 in order to have lungs segmented inside the patient

Usage: clitkExtractPatient [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
--imagetypes Display allowed image types (default=off)
-v --verbose Verbose (default=off)
--verboseStep Verbose each step (default=off)
-w --writeStep Write image at each step (default=off)
--verboseOption Display options values (default=off)
--verboseWarningOff Do not display warning (default=off)
--verboseMemory Display memory usage (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-a --afdb=STRING Output Anatomical Feature in a DB
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Binarize:
--lower=DOUBLE Initial lower threshold
--upper=DOUBLE Initial upper threshold (default=`-300')
--openingRadius=INT Radius for opening after threshold (default=`0')
<style="" & quot;text-align:center& quot; "">First Label Image (air=1):
--erode1 Decompose through erosion (default=off)
--radius1=INT Radius for erosion and dilation (default=`1')
--new1=INT Number of new labels (default=`1')
--max1=INT Max number of labels to consider (default=`2')
<style="" & quot;text-align:center& quot; "">Second Label Image (air=1):
--erode2 Decompose through erosion (default=off)
--radius2=INT Radius for erosion and dilation (default=`1')
--new2=INT Number of new labels (default=`1')
--max2=INT Max number of labels to consider (default=`2')
<style="" & quot;text-align:center& quot; "">Labels to keep (air=1):
--firstKeep=INT First label to keep (default=`1')
--lastKeep=INT Last label to keep (default=`1')
--remove=INT Labels to remove
<style="" & quot;text-align:center& quot; "">Clean-up:
--openClose Perform morphological opening and closing with unit radius (default=off)
--noAutoCrop If set : do no crop final mask to BoundingBox (default=off)

clitkExtrude

clitkExtrude 1.0

Extrude an image i along the last+1 dimension repeating the image N times. So the output has 1 dimension more than the input.

Usage: clitkExtrude [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-N --size=INT Size in pixel of extrusion (default=`1')
-s --spacing=DOUBLE Spacing of the new dimension (default=`1.0')
--origin=DOUBLE Origin of the new dimension (default=`0.0')
-l --like=STRING Size, spacing and origin like this image

clitkFlipImage

clitkFlipImage 1.0

Usage: clitkFlipImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-a --axe=INT Axe (default=`0')
--origin Flip around origin (default=off)

clitkGammaIndex

clitkGammaIndex 1.1

Compute the gamma index map for target dose map vs reference dose map. If verbose is given, the ratio of gamma>1 pixels of the total pixel in the image is computed. Absolute dose margin has priority over relative dose margin. The relative dose margin is relative to the maximum dose in the reference image.

clitkGammaIndex -v -i ref.mhd -j disp.mhd -o gamma.mhd -s 3 -r 0.04 this will compute the 3mm 4% gamma index between ref and disp.

Usage: clitkGammaIndex [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
-v --verbose Verbose (default=off)
-i --reference=STRING Reference dose map
-j --target=STRING Target dose map
-o --output=STRING Output image filename
-s --spatial-margin=DOUBLE Spatial margin [mm]
-r --relative-dose-margin=DOUBLE --relative-dose-margin=DOUBLEDose margin relative to max dose in reference [%]
-d --absolute-dose-margin=DOUBLE --absolute-dose-margin=DOUBLEAbsolute dose margin [Gray]
-x --translation-x=DOUBLE Target relative position x [mm] (default=`0')
-y --translation-y=DOUBLE Target relative position y [mm] (default=`0')
-z --translation-z=DOUBLE Target relative position z [mm] (default=`0')

clitkGateSimulation2Dicom

clitkGateSimulation2Dicom 1.0

Usage: clitkGateSimulation2Dicom [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-d --inputModelFilename=STRING --inputModelFilename=STRINGInput dicom model
-o --outputFilename=STRING Output dicom directory/filename

clitkHistogramImage

clitkHistogramImage 1.0

Save the histogram of the input image in the output text file

Usage: clitkHistogramImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output texte filename
-s --size=DOUBLE size of the bin

clitkImage2Dicom

clitkImage2Dicom 1.0

Convert the 3D mhd input image (int image) into a 3D dicom (outputDcm) based on the dictionary of the dicoms in inputDcm. The number of slice between the input and the inputDcm could be different

Usage: clitkImage2Dicom [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-d --inputDcm=STRING Input dicom filename
-o --outputDcm=STRING Output dicom folder
-n --nameDicom=STRING Output dicom filename
-u --newUID Write output with new UID (default=off)
--volume Save a dicom volume (default=off)
-k --key=STRING Keys of tags to modify
-t --tag=STRING Tags values

clitkImage2DicomDose

clitkImage2DicomDose 1.0

Convert mhd file into Dicom RTDose fil using a model

Usage: clitkImage2DicomDose [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING inputfile name
-m --DicomInputFile=STRING dicom model name
-o --output=STRING output directory/filename
-v --verbose Verbose (default=off)

clitkImageArithm

clitkImageArithm 1.0

Perform an arithmetic operation (+-*/ ...) using two images or using an image and a scalar value.

Usage: clitkImageArithm [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input1=STRING Input first image filename
-j --input2=STRING Input second image filename
-o --output=STRING Output image filename
-s --scalar=DOUBLE Scalar value
-t --operation=INT Type of operation : With another image : 0=add*, 1=multiply, 2=divide,3=max, 4=min, 5=absdiff, 6=squareddiff, 7=difference*, 8=relativ diff; For 'scalar' : 0=add*, 1=multiply*, 2=inverse,3=max, 4=min 5=absval 6=squareval7=ln 8=exp 9=sqrt 10=EPID 11=divide* 12=normalize (divide by max) 13=-ln(I/IO)**; * operations supported with vector fields as inputs. ** for fluence image, if pixel value == 0, consider value=0.5 (default=`0')
--pixelValue=DOUBLE Default value for NaN/Inf (default=`0.0')
-f --setFloatOutput Set output to float pixel type (default=off)

clitkImageConvert

clitkImageConvert 1.0

Convert an image into another image. Allow to change the file format and/or the pixel type. Known file formats 2D: jpeg png bmp tif mhd hdr vox dcm Known file formats 3D: mhd vox hdr dcm Known file formats 4D: mhd Known images: 2D 3D or 4D, schar, uchar, short, ushort, int, float and double

If the -o option is not given, the last parameter of the command line is used as output.

Usage: clitkImageConvert [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-t --type=STRING Output type (float, ushort ...)
-v --verbose Verbose (default=off)
-c --compression Compress output (default=off)
--vv Read image as in vv and save transform in meta information (default=off)
--correct Correct dicom with negative Z spacing (default=off)
--noniimeta Multiply 1st and 2nd coordinate of Direction and Origin by -1 (default=off)

clitkImageCreate

clitkImageCreate 1.0

Create a new singled value filled image (pixeltype is float, use clitkImageConvert to change).

Usage: clitkImageCreate [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-o --output=STRING Output image filename
-l --like=STRING Size/spacing like this other image
--size=INT Number of pixels of each coordinate
--spacing=FLOAT Spacing in mm between pixels
--origin=DOUBLE Origin in mm
--transformMatrix=DOUBLE Rotation matrix
--value=FLOAT Value for all voxels (default=`0.0')
-v --verbose Verbose (default=off)

clitkImageGradientMagnitude

clitkImageGradientMagnitude 1.0

Compute the gradient magnitude of the input image

Usage: clitkImageGradientMagnitude [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-m --mask=STRING Mask input image filename
-o --output=STRING Output image filename
-n --normalize Normalize the output image between 0 and 1 (default=off)
-g --gaussian_filter Gaussian filtering - default sigma value=1.0 (default=off)

clitkImageInfo

clitkImageInfo 1.0

Display information on images.

Usage: clitkImageInfo [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-l --long=INT Long line output (1 or 2) (default=`1')
-v --verbose Same as -l 1 (default=off)
-n --name Display filename (default=off)
-m --matrix Display matrix (default=off)

clitkImageIntensityWindowing

clitkImageIntensityWindowing 1.0

Usage: clitkImageIntensityWindowing [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-m --mask=STRING Mask input image filename

clitkImageLaplacian

clitkImageLaplacian 1.0

Compute the laplacian of the input image

Usage: clitkImageLaplacian [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-m --mask=STRING Mask input image filename
-o --output=STRING Output image filename
-n --normalize Normalize the output image between 0 and 1 (default=off)
-g --gaussian_filter Gaussian filtering - default sigma value=1.0 (default=on)

clitkImageMoment

clitkImageMoment 1.0

Calculate the image moment: the center of gravity

Usage: clitkImageMoment [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-c --center Compute center of gravity (default=on)
-s --second Compute second order moments (default=off)
-a --axes Compute the principal axes (default=off)

clitkImageStatistics

clitkImageStatistics 2.0

Compute statistics on an image, or on part of an image specified by a mask and label(s). The tool also supports multichannel images, which is useful, e.g., for vector fields. All channels are processed (separately) by default, but only one channel may be chosen.

Usage: clitkImageStatistics [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-c --channel=INT Image channel to be used in statistics (-1 to process all channels) (default=`-1')
-m --mask=STRING Mask image filename (uchar)
-l --label=INT Label(s) in the mask image to consider (default=`1')
--localize With verbose, write the index coordinates of the max and min (default=off)
--histogram=STRING Compute histogram, allows median calculation
--dvhistogram=STRING Compute dose volume histogram
--bins=INT Number of histogram bins (default=`100')
--lower=DOUBLE Lower histogram bound (default=`-1000')
--upper=DOUBLE Upper histogram bound (default=`1000')
-r --allow_resize Resize mask if different from input (default=off)

clitkImageToVectorImage

clitkImageToVectorImage 1.0

Compose 3 images to 1 vector image

Usage: clitkImageToVectorImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-o --output=STRING Output image filename

clitkImageUncertainty

clitk Compute the uncertainty of simulation outputs using Chetty's history-by-history's method

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input image filename
-s --inputSquared=STRING Input squared image filename
-o --output=STRING Output image filename
-n --NumberOfEvents=INT Number of events
-v --verbose Verbose (default=off)
-a --absolute Absolute instead of the relative (default=off)
-d --default=DOUBLE Default when input is 0. (default=`1.')

clitkInvertVF

clitk Read a DVF and invert it using a linear splat to the target, or by subsumpling the input grid and matching it to the output grid

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--threads=INT Number of threads (default=min(8, #CPU))
-i --input=STRING Input VF filename
-o --output=STRING Output VF filename
-t --type=INT Type of filter: 0=clitk (fast forward splat using linear kernels), 1=clitk (like 0, but input images are B-Spline coefficients), 2= itk (grid subsumpling with controllable precision) (default=`0')
--threadSafe Clitk: use thread safe algorithm (default=off)
-p --pad=DOUBLE Clitk: edge padding value (1 or N number of values!, defautls to zeros)
-s --sampling=INT Itk: subsampling factor (default=`20')
-l --like=STRING Image whose grid (spacing and size) will be used for output

clitkJacobianImage

clitk Read a DVF and calculate the corresponding jacobian image.

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input VF filename
-o --output=STRING Output VF filename

clitkMaskLandmarks

clitkMaskLandmarks 1.0

Remove landmarks outside of a given mask also remove their corresponding points if multiple input are given.

Usage: clitkMaskLandmarks [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input landmarks filename
-m --mask=STRING Input mask
-o --output=STRING Output landmarks filename

clitkMaskOfIntegratedIntensity

clitkMaskOfIntegratedIntensity 1.0

Compute a mask that represent X% of the total pixels values

Usage: clitkMaskOfIntegratedIntensity [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-p --percentage=DOUBLE Percentage of total pixels values (in %)

clitkMatrixInverse

clitkMatrixInverse 1.0

Usage: clitkMatrixInverse [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input matrix filename
-o --output=STRING Output matrix filename

clitkMatrixMultiply

clitkMatrixMultiply 1.0

Multiply two 4x4 matrices. In matrice notations, does input2*input

Usage: clitkMatrixMultiply [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input1=STRING Input matrix filename
-j --input2=STRING Input matrix filename
-o --output=STRING Output matrix filename

clitkMatrixToElastixTransform

clitkMatrixToElastixTransform 1.0

Usage: clitkMatrixToElastixTransform [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input matrix filename
-o --output=STRING Output elastix filename
--center=FLOAT Rotation center

clitkMatrixTransformToVF

clitkMatrixTransformToVF 1.0

Convert a matrix to a DVF with given properties

Usage: clitkMatrixTransformToVF [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --matrix=STRING Input matrix filename
-o --output=STRING Output image filename
-d --dim=INT Dimension (default=`3')
<style="" & quot;text-align:center& quot; "">Output Image Properties:
--like=STRING Make output like this image
--origin=DOUBLE Origin for the output image (default=`0.0')
--size=INT Size for the output image (default=`100')
--spacing=DOUBLE Spacing for the output image (default=`1.0')

clitkMedianImageFilter

clitkMedianImageFilter 1.0

Usage: clitkMedianImageFilter [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-r --radius=INT Radius in each Direction (default=`1')

clitkMedianTemporalDimension

clitkMedianTemporalDimension 1.0

Average the last dimension to an (n-1)D image. Input is either nD or multiple (n-1)D image or DVF

Usage: clitkMedianTemporalDimension [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename

clitkMergeAsciiDoseActor

clitk Add values from two ASCII files (must contains list of numbers)

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input1=STRING Input ASCII file
-j --input2=STRING Input ASCII file
-o --output=STRING Output ASCII file

clitkMergeRootFiles

clitkMergeRootFiles 1.0

Merge several ROOT files

Usage: clitkMergeRootFiles [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input ROOT filenames
-o --output=STRING Output ROOT filename
-f --fastmerge Fast merge
-v --verbose=INT Verbose level

clitkMergeSequence

clitkMergeSequence 1.0

Read a series of nD images (unnamed inputs) and merge them to a (n+1)D image. The spacing of the (n+1)th dimension is given by the option spacing.

Usage: clitkMergeSequence [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-s --spacing=DOUBLE Spacing for the new dimension (default=`1')
-o --output=STRING Output filename
-v --verbose Verbose (default=off)

clitkMinMaxMask

clitkMinMaxMask 1.0

ssdfgsfg ssdf g.

Usage: clitkMinMaxMask [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input1=STRING Input mask image filename
-j --input2=STRING Input mask image filename

clitkMIP

clitkMIP 1.0

Usage: clitkMIP [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-d --dimension=INT Dimension along which to project

clitkMirrorPadImage

clitkMirrorPadImage 1.0

Usage: clitkMirrorPadImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-m --mirror=INT Mirror the entire image along given axis
-p --pad=INT Mirror pad with given size
-l --lower Pad on lower end (else upper) (default=off)
--origin Set new origin to 0 (default=off)

clitkMorphoMath

clitk Perform standard morphological operations

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
<style="" & quot;text-align:center& quot; "">Input:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Processing Parameters:
-t --type=INT 0=Erode, 1=Dilate, 2=Close (erode(dilate(x))), 3=Open (dilate(erode(x))), 4=CondErode, 5=CondDilate (default=`0')
--fg=FLOAT Foreground value (default=`1')
--bg=FLOAT Background value (0,1,3: filling value) (default=`0')
-b --bound 0-1: Set borders to foreground/ 2:safe borders (default=off)
-r --radius=INT Use binary ball element with given radius (default=`1')
-m --radiusInMM=DOUBLE Use binary ball element with given radius in mm (rounded to nearest voxel value), you can give one radius by dimension (default=`1')
--extend Extend the image size according to radius (default=off)

clitkMotionMask

clitkMotionMask 1.0

From an input CT image (HU), extract feature images (air, ribs and lungs) and calculate the motion mask using levelsets, Vandemeulebroucke2010, ICCR. More elaborate methods for extracting the feature images have been incude in clitkExtract*, with *=Lungs,Bones,Patient.

Usage: clitkMotionMask [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-m --monitor=STRING Monitoring image for levelsets
--spacing=DOUBLE Low dimensional spacing to perform initial level set steps (default=`4')
<style="" & quot;text-align:center& quot; "">Feature Images (feature=1,rest=0). Set them or extract them from the input:
--featureAir=STRING Input feature image
--lowerThresholdAir=DOUBLE --lowerThresholdAir=DOUBLELower threshold for air feature image extraction (default=`-10000')
--upperThresholdAir=DOUBLE --upperThresholdAir=DOUBLEUpper threshold for air feature image extraction (default=`-800')
--pad Make a border of air around the image (for cropped images) (default=off)
--featureBones=STRING Input feature image
--lowerThresholdBones=DOUBLE --lowerThresholdBones=DOUBLELower threshold for bones feature image extraction (default=`100')
--upperThresholdBones=DOUBLE --upperThresholdBones=DOUBLEUpper threshold for bones feature image extraction (default=`1000')
--featureLungs=STRING Input feature image
--lowerThresholdLungs=DOUBLE --lowerThresholdLungs=DOUBLELower threshold for lungs feature image extraction (default=`-950')
--upperThresholdLungs=DOUBLE --upperThresholdLungs=DOUBLEUpper threshold for lungs feature image extraction (default=`-600')
--writeFeature=STRING Write the combined feature image
<style="" & quot;text-align:center& quot; "">Ellipsoide initialization:
--ellips=STRING Input ellipsoide image (=1, at half resolution)
--writeEllips=STRING Write the initial ellipsoide image
--writeDistMap=STRING Write the distance map
--ellipseAutoDetect Auto-detect offset and axes of initial ellipse (default=off)
--offset=DOUBLE Offset for ellips center from body center of gravity (default= 0,-50,0 mm)
--axes=DOUBLE Half axes of the ellips (default= 100,30,150)
<style="" & quot;text-align:center& quot; "">Ellipsoide growing:
--grownEllips=STRING Input grown ellips image (=1, at half resolution)
--offsetDetect=DOUBLE Offset of detection point from abdomen (default= 0,-10,0 mm)
--detectionPairs=STRING Additional images to detect the abdomen (eg end-inhalation frame). The most anterior point will be retained.
--detectionPoint=DOUBLE Physical coordinates of the detection point from abdomen (default= 0,-10,0 mm)
--curve1=DOUBLE Curvature for this levelset (default=`35.0')
--maxRMS1=DOUBLE Tolerance for this levelset (default=`0.001')
--iter1=INT Iterations performed between monitoring (default=`50')
--writeGrownEllips=STRING Write the grown ellipsoide image
<style="" & quot;text-align:center& quot; "">Filling the bones image:
--filledRibs=STRING Input filled rib image (=1, at half resolution)
--fillingLevel=DOUBLE Minimum lung fill level: [0,100] % (default=`98.0')
--curve2=DOUBLE Curvature for this levelset (default=`30.0')
--maxRMS2=DOUBLE Tolerance for this levelset (default=`0.001')
--iter2=INT Iterations performed between monitoring (default=`50')
--writeFilledRibs=STRING Write the filled ribs image image
<style="" & quot;text-align:center& quot; "">Collapsing to the lung image:
--curve3=DOUBLE Curvature for this levelset (default=`30.0')
--prop3=DOUBLE Propagation for this levelset (default=`0')
--maxRMS3=DOUBLE Tolerance for this levelset (default=`0.001')
--iter3=INT Iterations performed between monitoring (default=`20')
--maxIter3=INT Iterations performed between monitoring (default=`500')
<style="" & quot;text-align:center& quot; "">Clean-up:
--openClose Perform morphological opening and closing with unit radius (default=on)

clitkNormalizeImageFilter

clitkNormalizeImageFilter 1.0

Usage: clitkNormalizeImageFilter [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-m --mask=STRING Mask input image filename
-n --total_normalisation Normalise such as the total is = 1.0 (default=off)

clitkNVectorImageTo4DImage

clitkNVectorImageTo4DImage 1.0

Convert all pixel channels of the image into a 4D image

Usage: clitkNVectorImageTo4DImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename

clitkPadImage

clitkPadImage 1.0

Pad an image according to a given extends or like another image

Usage: clitkPadImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Used determined padding:
-l --lower=INT Size of the lower bound padding (multiple values=number of image dimension)
-u --upper=INT Size of the upper bound padding (multiple values=number of image dimension)
<style="" & quot;text-align:center& quot; "">Pad like another image:
--like=STRING Pad like this image (must have the same spacing and bounding box must be larger)
<style="" & quot;text-align:center& quot; "">Extra parameters:
--value=FLOAT Value to be set in padded area (default=`0')

clitkPartitionEnergyWindowDicom

clitkPartitionEnergyWindowDicom 1.0

From one Dicom with different energy windows (eg with SPECT), the tool create new dicoms for each energy window and copy the correct dicom tag

Usage: clitkPartitionEnergyWindowDicom [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input Dicom image filename
-o --output=STRING Output dicom directory

clitkProfileImage

clitkProfileImage 1.0

Save the profile between 2 points of the input image in the output text file

Usage: clitkProfileImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output texte filename
-f --point1=DOUBLE First point (vox)
-s --point2=DOUBLE Second point (vox)

clitkRegionGrowing

clitkRegionGrowing 1.0

Region growing from a seed point using various types of conditions to control the growing

Usage: clitkRegionGrowing [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filename
<style="" & quot;text-align:center& quot; "">Parameters:
-t --type=INT Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3=locally-adaptive-threshold, 4=explosion-controlled-threshold (default=`0')
-l --lower=DOUBLE Lower threshold value (default=`310')
-u --upper=DOUBLE Upper threshold value (default=`4000')
-s --seed=INT Seed index postion (in voxels) (default=`0')
--seedRadius=INT Radius used for seed dilatation(in voxel) (default=`0')
-p --pad=DOUBLE The replace padding value (default=`1.0')
-r --radius=INT 1-3: The radius of the neighborhood (default=`1')
--iter=INT 2: Iterations (default=`5')
-m --multiplier=DOUBLE 2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times (default=`2.0')
--maxSD=DOUBLE 3: Limit to SD
--adaptLower 3,4: (locally) adapt lower thresholding (default=off)
--adaptUpper 3,4: (locally) adapt upper thresholding (default=off)
--maxUpper=DOUBLE 4: Maximum upper threshold value (default=`2000')
--minLower=DOUBLE 4: Minimum lower threshold value (default=`-1000')
--step=DOUBLE 4: Threshold step size (default=`64.0')
--minStep=DOUBLE 4: Minimum threshold step size (default=`1')
--full 4: use full connectivity (not implemented yet) (default=off)

clitkRTStructStatistics

clitkRTStructStatistics 2.0

Find the centroid (in mm) and roundness of a binarized image.

Usage: clitkRTStructStatistics [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename (mask)

clitkScintivolStats

clitkScintivolStats 1.0

Convert an image into another image. Allow to change the file format and/or the pixel type. Known file formats 2D: jpeg png bmp tif mhd hdr vox dcm Known file formats 3D: mhd vox hdr dcm Known file formats 4D: mhd Known images: 2D 3D or 4D, schar, uchar, short, ushort, int, float and double

If the -o option is not given, the last parameter of the command line is used as output.

Usage: clitkScintivolStats [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-o --output=STRING Output .csv filename
--append Append results to .csv file (eg: for scatter) (default=off)
--dynamic1=STRING Dynamique 1 filename (geometrical mean)
--frameDurationDynamic1=DOUBLE --frameDurationDynamic1=DOUBLEFrame duration for dynamique 1
--heartMask=STRING Heart mask filename
--liverMask=STRING Liver mask filename
--dynamic2=STRING Dynamique 2 filename (geometrical mean)
--frameDurationDynamic2=DOUBLE --frameDurationDynamic2=DOUBLEFrame duration for dynamique 2
--acquisitionTimeDynamic2=DOUBLE --acquisitionTimeDynamic2=DOUBLEStart acquisition time of the dynamic2 after dynamic1
--parenchymaMask=STRING Parenchyma mask filename
--tomo=STRING Tomo image filename
--acquisitionTimeTomo=DOUBLE --acquisitionTimeTomo=DOUBLEAcquisition time for tomo
--totalLiverMask=STRING Total liver mask filename
--remnantLiverMask=STRING Remnant liver mask filename

clitkSetBackground

clitkSetBackground 1.0

Usage: clitkSetBackground [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-m --mask=STRING Mask image filename
-p --outsideValue=DOUBLE Outside value (default=`0.0')
-l --maskValue=DOUBLE Mask value (default=`0.0')
--fg Foreground mode (default=off)

clitkSpect2Dicom

clitkSpect2Dicom 1.0

Convert the 3D mhd input SPECT image (int image) into a 3D dicom (outputDcm) based on the dictionary of the dicoms in inputDcm.

Usage: clitkSpect2Dicom [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-d --inputDcm=STRING Input dicom filename
-o --outputDcm=STRING Output dicom filename

clitkSplitImage

clitkSplitImage 1.0

Split an image into n images along a dimension

Usage: clitkSplitImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input image filename
-o --output=STRING Output image base filename
-v --verbose Verbose (default=off)
-d --dimension=INT Dimension to split on
-p --png Png file format (default=off)
-w --window=DOUBLE Window
-l --level=DOUBLE Level

clitkSum

clitkSum 1.0

Usage: clitkSum [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-d --dimension=INT Dimension along which to sum

clitkSUVPeak

clitkSUVPeak 2.0

This tool Compute the SUV Peak. The output is the position of the SUV Peak (in mm) and its value. The filter use a normalized sphere of 1 cc with 1 for voxel inside, 0 for outside. And for voxels that intercepted the sphere, it computes the intersection volume using Monte Carlo simulation.

Usage: clitkSUVPeak [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input first image filename
-m --mask=STRING Mask image filename (uchar)
-r --allow_resize Resize mask if different from input (default=off)
--volume=DOUBLE Volume of the filter in cc (default=`1')

clitkTransformLandmarks

clitkTransformLandmarks 1.0

Trasnform a set of landmarks with the given 4x4 matrix. Output to stdout.

Usage: clitkTransformLandmarks [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input landmarks filename
-m --matrix=STRING Input 4x4 matrix filename ('.mat' file)
-s --spacing=DOUBLE If given, applies the given spacing (x,y,z) to the input points. (default=`1')
-o --output=STRING Output landmarks filename
-t --type=STRING Landmarks type ('pts' for Jef; 'txt' for VV ; 'vtk' for vtk meshes) (default=`txt')

clitkUnsharpMask

clitkUnsharpMask 1.0

Image sharpening technique. It computes Image - blurred(Image). Here blurred(Image) is the output of a gaussian filtering with a sigma measured in world coordinates

Usage: clitkUnsharpMask [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-s --sigma=DOUBLE Sigma of the gaussian

clitkUpdateVRTagDicom

clitkUpdateVRTagDicom 1.0

Fix VR Dicom tag mistakes with gdcm

Usage: clitkUpdateVRTagDicom [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input Dicom image filename
-o --output=STRING Output dicom filename
-m --model=STRING Model dicom filename

clitkVectorArithm

clitkVectorArithm 1.0

Perform an arithmetic operation (+-*/ ...) using two images or using an image and a scalar value.

Usage: clitkVectorArithm [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
--imagetypes Display allowed image types (default=off)
-i --input1=STRING Input first image filename
-j --input2=STRING Input second image filename
-o --output=STRING Output image filename
-s --scalar=DOUBLE Scalar value
-t --operation=INT Type of operation : With another image : 0=add, 1=multiply, 2=dotproduct, 7=difference, 9=crossproduct; For 'scalar' : 0=add, 1=multiply, 5=absval (magnitude), 6=squared magnitude, 11=divide, 12=normalize (default=`0')
--pixelValue=DOUBLE Default value for NaN/Inf (default=`0.0')
-f --setFloatOutput Set output to float pixel type (default=off)

clitkVectorImageToImage

clitkVectorImageToImage 1.0

Extract a component image from a vector image

Usage: clitkVectorImageToImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-c --componentIndex=INT Component index to extract (default=`0')

clitkVFConvert

clitkVFConvert 1.0

Convert file format

Usage: clitkVFConvert [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-o --output=STRING Output image filename

clitkVFInterpolate

clitkImageInterpolate 1.0

Interpolate an image. You can specify the interpolation, you can apply a Gaussian filter before.

Usage: clitkImageInterpolate [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input1=STRING Input image filename
-j --input2=STRING Input image filename
-o --output=STRING Output image filename
-d --distance=FLOAT Distance (d in [0,1])
-v --verbose Verbose (default=off)
--interp=STRING Interpolation type: {nn, linear} (default=`nn')

clitkVFResample

clitkImageResample 1.0

Resample an image. You can specify the interpolation, you can apply a Gaussian filter before.

Usage: clitkImageResample [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input image filename
-o --output=STRING Output image filename
-v --verbose Verbose (default=off)
--interp=STRING Interpolation type: {nn, linear, bspline, blut} (default=`nn')
-b --order=INT BSpline ordre (range 0-5) (default=`3')
-s --sampling=INT BLUT sampling value (default=`30')
--size=INT Number of pixels of each coordonate (default=`0')
--spacing=FLOAT Spacing in mm between pixels (default=`0.0')
-g --gauss=FLOAT Apply Gaussian before (sigma in mm) ; no Gaussian if not given (default=`1.0')
-d --default=FLOAT Default pixel value (default=`0.0')

clitkWarpImage

clitkWarpImage 1.0

Warp an image. Output will have the extent (origin+ spacing*size) of the input.

Usage: clitkWarpImage [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
<style="" & quot;text-align:center& quot; "">I/O:
-i --input=STRING Input image filename
-o --output=STRING Output image filenameGroup: DVFoptionan option of this group is required
--vf=STRING Vector field filename
--coeff=STRING B-Spline coefficients filename
<style="" & quot;text-align:center& quot; "">Options:
-f --forward Use forward warping (only linear interp) (default=off)
-s --spacing=INT The output spacing: 0=like the VF, 1= like the input image (interpolation of the VF prior to warp) (default=`0')
--pad=FLOAT Edge padding value (default=`0.0')
<style="" & quot;text-align:center& quot; "">Interpolation: for image intensity and prior resampling of DVF:
--interp=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpSF=INT Sampling factor if BLUT (default=`20')
--interpVF=INT Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT (default=`1')
--interpVFOrder=INT Order if BLUT or BSpline (0-5) (default=`3')
--interpVFSF=INT Sampling factor if BLUT (default=`20')

clitkWriteDicomSeries

clitkWriteDicomSeries 1.0

Usage: clitkWriteDicomSeries [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-v --verbose Verbose (default=off)
-i --input=STRING Input image filename
-d --inputDir=STRING Input dicom directory
-o --outputDir=STRING Output dicom directory
-k --key=STRING Keys of tags to modify (default=`0008
-t --tag=STRING Tags values (default=`MIDPOSITION')
-e --newSeriesUID Write the series with a new series UID (ignored if given in key/tag option) (default=off)
-u --newStudyUID Write the series with a new study UID (ignored if given in key/tag option; forces newSeriesUID = true) (default=off)
-s --useSizeAsReference Use the size of the dicom image as reference for an occasional resampling (default=off)
-p --preserve Preserve private tags and keep original UID (eg: Xio) (default=off)

clitkZeroVF

clitk Read a vector fields (.mhd, .vf, ..) and zero it

Usage: clitk [OPTIONS]... [FILES]...
-h --help Print help and exit
-V --version Print version and exit
--config=STRING Config file
-i --input=STRING Input VF filename
-o --output=STRING Output VF filename
-v --verbose Verbose (default=off)