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.