Provided by: cmtk_3.3.1p1+dfsg-2build1_amd64 bug

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.

       --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 <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. 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.

   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.

       --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.

   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.

       --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

   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]

       --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.

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.