Provided by: cmtk_3.0.0-1ubuntu1_amd64
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 <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/Transformation Database --db <string> Path to image/transformation database that should be updated with the newly created image. [Default: NONE] Input Image Controls --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. 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 <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. 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 <string> Binary mask file name: eliminate all image pixels where mask is 0. --mask-inverse <string> Inverse binary mask file name eliminate all image pixels where mask is NOT 0. --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. Intensity Transformations --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. Morphological Operations --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. --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 Filter Operations --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. Grid Operations --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] --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.
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.