GlobalToolkitOptions(thesearesharedbyallCMTKtools)--help
Write list of basic command line options to standard output.
--help-all
Write complete list of basic and advanced command line options to standard output.
--wiki
Write list of command line options to standard output in MediaWiki markup.
--man
Write man page source in 'nroff' markup to standard output.
--version
Write toolkit version to standard output.
--echo
Write the current command line to standard output.
--verbose-level<integer>
Set verbosity level.
--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
--threads<integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).
Image/TransformationDatabase--db<string>
Path to image/transformation database that should be updated with the newly created image.
[Default:NONE]InputImageControls--set-padding<double>
Set padding value: all pixels in the input image that have this value will be ignored in all
subsequent operations.
--unset-padding
Unset padding value: for all subsequent operations, all pixels will be treated according to their
value.
--labels
Specify that the image values are to be treated as discrete labels. This will result in the
appropriate intent code to be set in output files in NIfTI format.
--grey
Specify that the image values are to be treated as continuous grey levels. This will reset the
intent code in files read from NIfTI format.
DataTypeConversion--char
8 bits, signed integer
--byte
8 bits, unsigned integer
--short
16 bits, signed integer
--ushort
16 bits, unsigned integer
--int
32 bits signed integer
--uint
32 bits unsigned integer
--float
32 bits floating point
--double
64 bits floating point
ValueMappings--map-values<string>
Apply mapping function to pixel values. Mapping is defined as 'VAL0[,VAL1,...][:NEWVAL]' to map
values VAL0, VAL1, etc. to new value NEWVAL. If NEWVAL is not given, values are set to padding.
--map-values-only<string>
Apply mapping function to pixel values and replace unmapped pixels with padding. Multiple such
mapping rules can be concatenated as RULE0+RULE1[+...]; all concatenated rules will be applied
simultaneously.Mapping is defined as 'VAL0[,VAL1,...][:NEWVAL]' to map values VAL0, VAL1, etc. to
new value NEWVAL. If NEWVAL is not given, values are set to padding. Multiple such mapping rules can
be concatenated as RULE0+RULE1[+...]; all concatenated rules will be applied simultaneously.
--replace-padding<double>
Replace padded pixel data with given value.
--replace-inf-nan<double>
Replace all infinite and not-a-number pixels with given value.
ImageFlipping--flip-x
Flip (mirror) along x-direction
--flip-y
Flip (mirror) along y-direction
--flip-z
Flip (mirror) along z-direction
ImageMaskingandThresholding--mask<string>
Binary mask file name: eliminate all image pixels where mask is 0. Masked-out pixels will NOT be set
to zero, but will instead be replaced with the currently-set padding value. Use '--set-padding 0'
prior to '--mask' to force setting to zero.
--mask-inverse<string>
Inverse binary mask file name eliminate all image pixels where mask is NOT 0. See also notes
regarding padding under '--mask' above.
--thresh-below<double>
Set all values below threshold to threshold value.
--thresh-above<double>
Set all values above threshold to threshold value.
--thresh-below-to-padding<double>
Set all values below threshold to padding value.
--thresh-above-to-padding<double>
Set all values above threshold to padding value.
--binarize-thresh<double>
Set all values below threshold to 0, all values equal or above to 1.
--otsu-thresh
Binarize image to 0/1 using threshold computed with Otsu's method. Argument is number of histogram
bins for threshold computation.
--otsu-thresh-nbins<integer>
Binarization using Otsu's method with user-defined number of histogram bins for threshold
computation.
--prune-histogram<integer>
Threshold image by 'intensity histogram pruning', i.e., for given argument n [histogram bins]
determine thresholds such that the 1/n-th fraction of highest and lowest voxels are thresholded.
--prune-histogram-high<integer>
Like '--prune-histograms', but only remove high intensities.
--prune-histogram-low<integer>
Like '--prune-histograms', but only remove low intensities.
IntensityTransformations--scale-to-range<string>
Scale image intensities to range 'from:to', e.g., '0:255' before conversion to byte data.
--histogram-equalization
Apply histogram equalization.
--histogram-equalization-nbins<integer>
Apply histogram equalization with <int> number of bins.
--match-histograms<string>
Transform intensities to match the distribution in the image provided as the argument for this
command.
--match-mean-sdev<string>
Scale intensities to match the mean and standard distribution of intensities in the image provided
as the argument for this command.
MorphologicalOperations--revert
Revert a binary mask, i.e., exchange foreground and background.
--erode<integer>
Morphological erosion operator (by pixels)
--dilate<integer>
Morphological dilation operator (by pixels)
--erode-distance<double>
Morphological erosion operator (by distance). Often preferable for anisotropic data.
--erode-distance-multilabel<double>
Morphological erosion operator (by distance) for multi-label maps. The result will be either byte,
unsigned short, or unsigned int data, depending on the index of the largest used label in the input.
--dilate-distance<double>
Morphological dilation operator (by distance). Oftern preferable for anisotropic data.
--connected-components
Create connected components map with regions numbered by decreasing component size
--boundary-map
Create boundary map
--multi-boundary-map
Create multi-valued boundary map
--distance-map
Compute unsigned Euclidean distance map. Input image is interpreted as binary mask.
--signed-distance-map
Compute signed (inside=negative, outside=positive) Euclidean distance map
FilterOperations--median-filter<string>
Median filter. This operation takes the filter radius in pixels as the parameter. A single integer
defines the kernel radius in all three dimensions. Three comma-separated integers define separate
radii for the three dimensions.
--mean-filter<string>
Regional mean filter. This operation takes the filter radius in pixels as the parameter. A single
integer defines the kernel radius in all three dimensions. Three comma-separated integers define
separate radii for the three dimensions.
--fast-mean-filter<string>
Regional mean filter (fast, linear time implementation). This operation takes the filter radius in
pixels as the parameter. A single integer defines the kernel radius in all three dimensions. Three
comma-separated integers define separate radii for the three dimensions.
--variance-filter<string>
Regional variance filter. This operation takes the filter radius in pixels as the parameter. A
single integer defines the kernel radius in all three dimensions. Three comma-separated integers
define separate radii for the three dimensions.
--fast-variance-filter<string>
Fast (linear-time) regional variance filter. This operation takes the filter radius in pixels as the
parameter. A single integer defines the kernel radius in all three dimensions. Three comma-separated
integers define separate radii for the three dimensions.
--third-moment-filter<string>
Regional third moment filter. This operation takes the filter radius in pixels as the parameter. A
single integer defines the kernel radius in all three dimensions. Three comma-separated integers
define separate radii for the three dimensions.
--standard-deviation-filter<string>
Regional standard deviation filter. This operation takes the filter radius in pixels as the
parameter. A single integer defines the kernel radius in all three dimensions. Three comma-separated
integers define separate radii for the three dimensions.
--smoothness-filter<string>
Regional 'smoothness' filter. This operation takes the filter radius in pixels as the parameter. A
single integer defines the kernel radius in all three dimensions. Three comma-separated integers
define separate radii for the three dimensions.
--gaussian-filter-sigma<double>
Filter image with Gaussian kernel. This operation takes a single real-valued parameter, which
specifies the kernel coefficient sigma in world units [e.g., mm] as the parameter.
--gaussian-filter-fwhm<double>
Filter image with Gaussian kernel. This operation takes a single real-valued parameter, which
specifies the kernel full width at half maximum in world units [e.g., mm].
--laplace-filter
Filter image with edge-enhancing Laplacian kernel.
GridOperations--downsample-select<string>
Downsample image by pixel selection using per-axis factors 'Fx,Fy,Fz' or using single factor 'Fxyz'
--downsample-average<string>
Downsample image by averaging using per-axis factors 'Fx,Fy,Fz' or using single factor 'Fxyz'
--resample<double>
Resample image to near-isotropic pixels while preserving the image field-of-view. Takes one
argument, the target resolution in world units [e.g., mm]
--resample-exact<double>
Resample image to exactly isotropic pixels of the given resolution while matching the image field-
of-view as closely as possible. Takes one argument, the target resolution in world units [e.g., mm]
--crop-by-index<string>
Crop image to a region specified by a set of six grid index coordinates given as comma-separated
integers x0,y0,z0,x1,y1,z1
--crop-by-threshold<double>
Crop image to region determined via a given threshold. The resulting image will contain all pixels
larger than the given parameter.
--crop-by-threshold-write-region<double>
Crop image to region determined via a given threshold and write cropping region to standard output.
--crop-by-threshold-write-xform<double>
Crop image to region determined via a given threshold and write cropping transformation to standard
output.
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