--- name: "cmtk-convertx" section: "1" platform: "linux" package: "cmtk" version: "3.3.1p2+dfsg-3" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/cmtk-convertx" --- # cmtk-convertx(1) Convert between image file formats and data types. ## NAME convertx - Convert between image file formats and data types. ## SYNOPSIS convertx \[options\] infile outfile ## DESCRIPTION This tool converts between image file formats and pixel data types. It can also apply simple, general-purpose image operations in the process. An arbitrary number of operations can be specified on the command line, which will be applied exactly in the order given. ## OPTIONS ### Global Toolkit Options (these are shared by all CMTK tools) - **--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** *\* Set verbosity level. - **--verbose**, **-v** Increment verbosity level by 1 (deprecated; supported for backward compatibility). - **--threads** *\* Set maximum number of parallel threads (for POSIX threads and OpenMP). ### Image/Transformation Database - **--db** *\* Path to image/transformation database that should be updated with the newly created image. **\[Default: NONE\]** ### Input Image Controls - **--set-padding** *\* 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. ### Data Type Conversion - **--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 ### Value Mappings - **--map-values** *\* 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** *\* 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** *\* Replace padded pixel data with given value. - **--replace-inf-nan** *\* Replace all infinite and not-a-number pixels with given value. ### Image Flipping - **--flip-x** Flip (mirror) along x-direction - **--flip-y** Flip (mirror) along y-direction - **--flip-z** Flip (mirror) along z-direction ### Image Masking and Thresholding - **--mask** *\* 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** *\* Inverse binary mask file name eliminate all image pixels where mask is NOT 0. See also notes regarding padding under '--mask' above. - **--thresh-below** *\* Set all values below threshold to threshold value. - **--thresh-above** *\* Set all values above threshold to threshold value. - **--thresh-below-to-padding** *\* Set all values below threshold to padding value. - **--thresh-above-to-padding** *\* Set all values above threshold to padding value. - **--binarize-thresh** *\* 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** *\* Binarization using Otsu's method with user-defined number of histogram bins for threshold computation. - **--prune-histogram** *\* 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** *\* Like '--prune-histograms', but only remove high intensities. - **--prune-histogram-low** *\* Like '--prune-histograms', but only remove low intensities. ### Intensity Transformations - **--scale-to-range** *\* Scale image intensities to range 'from:to', e.g., '0:255' before conversion to byte data. - **--histogram-equalization** Apply histogram equalization. - **--histogram-equalization-nbins** *\* Apply histogram equalization with \ number of bins. - **--match-histograms** *\* Transform intensities to match the distribution in the image provided as the argument for this command. - **--match-mean-sdev** *\* Scale intensities to match the mean and standard distribution of intensities in the image provided as the argument for this command. ### Morphological Operations - **--revert** Revert a binary mask, i.e., exchange foreground and background. - **--erode** *\* Morphological erosion operator (by pixels) - **--dilate** *\* Morphological dilation operator (by pixels) - **--erode-distance** *\* Morphological erosion operator (by distance). Often preferable for anisotropic data. - **--erode-distance-multilabel** *\* 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** *\* 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 ### Filter Operations - **--median-filter** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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. ### Grid Operations - **--downsample-select** *\* Downsample image by pixel selection using per-axis factors 'Fx,Fy,Fz' or using single factor 'Fxyz' - **--downsample-average** *\* Downsample image by averaging using per-axis factors 'Fx,Fy,Fz' or using single factor 'Fxyz' - **--resample** *\* 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** *\* 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** *\* 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** *\* 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** *\* Crop image to region determined via a given threshold and write cropping region to standard output. - **--crop-by-threshold-write-xform** *\* Crop image to region determined via a given threshold and write cropping transformation to standard output. ## AUTHORS Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko ## LICENSE http://www.fsf.org/licensing/licenses/gpl.html ## BUGS Report bugs at http://nitrc.org/projects/cmtk/ ## ACKNOWLEDGMENTS CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.