Provided by: cmtk_2.1.0-1_amd64 bug

NAME

       cmtk - the Computational Morphometry Toolkit

SYNOPSIS

       cmtk <command> [options]

DESCRIPTION

       This  helper  script provides a unified access to all command line tools provided by CMTK.
       Please specify CMTK's command to run and its options.  See  cmtk-<command>(1)  manpage  or
       output of cmtk <command> --help for <command> specific options

COMMANDS

       asegment
            Register  a  target  image  to  an  atlas, using affine followed by nonrigid B-spline
            registration, then reformat the atlas label map to the target image.

       asegment_sri24
            Register a target image to a selected channel of the SRI24 atlas, then  reformat  one
            of the atlas label maps to the target image.

       average_affine
            This  tool  computes  the  average  of  a sequence of user-provided affine coordinate
            transformations.

       average_edt
            Average segmentations (label fields) using the Euclidean Distance Transform.

       average_images
            This tool computes pixelwiase average,  variance,  standard  deviation,  z-score,  or
            entropy images from a list of user-provided intensity images.

       average_labels
            Average co-registered label images using partial volumes

       avg_adm
            Compute  average-shape  average-intensity images and deformation maps using an active
            deformation model.

       concat_affine
            This  tool  computes  the  explicit  concatenation  of  multiple  affine   coordinate
            transformations, each of which can be optionally inverted.

       convert_warp
            This   tool   converts   nonrigid   BB-spline   free-format   deformation  coordinate
            transformations  between  different  representations  (e.g.,  absolute  vs.  relative
            vectors). Also creates fractional transformations.

       convertx
            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.

       dbtool
            This tool modifies and queries the database of  images  and  transformations  between
            them.

       dcm2image
            Combine sets of DICOM slices to 3D image stacks

       describe
            This tool prints a detailed description of the input image(s)

       destripe
            This program corrects stripe artifacts in acquired image stacks which can result from
            between-slice intensity scale differences.

       film This tool splits an interleaved input image into the pass images, co-registers  them,
            and reconstructs a motion-corrected image

       filter
            This   tool   applies   spatial   filtering  operators,  including  cnotent-sensitive
            opersators, based on selective Gaussian kernels.

       fview

       glm  Statistical modeling of pixel intensities in multiple images using a  General  Linear
            Model.

       gregxform
            This  tool reads a list of 3D coordinates and applies a coordimnate transformation to
            them. The transformation can optionally be inverted. The transformed coordinates  are
            then written to standard output.

       groupwise_affine
            This  tool registers a population of input images simultaneously, without a template,
            using either the 'congealing' algorithm or a groupwise similarity measure based on  a
            continuous approximation of mutual information ('RMI').

       groupwise_init
            Compute initial affine alignment for a group of input images, which can be used as an
            input for groupwise registration

       groupwise_warp
            This tool nonrigidly registers a population of input images simultaneously, without a
            template,  using  either the 'congealing' algorithm or a groupwise similarity measure
            based on a continuous approximation of mutual information ('RMI').

       hausdorff
            This tool computes the Hausdorff distance between two label images.

       histogram
            Create a histogram of image intensities and  write  as  tab-separated  text  file  to
            standard output

       imagemath
            Perform operations on images using stack-based postfix notation.

       jidb This  tool splits an interleaved input image into the pass images, co-registers them,
            and reconstructs a motion-corrected image

       levelset
            Levelset-type segmentation of foreground/background using minimum  regional  variance
            energy

       make_initial_affine
            Compute initial affine transformation by aligning centers of mass or principal axes

       mat2dof
            Convert transformation matrix to degrees of freedom

       mcaffine
            Multi-channel  affine  image  registration  using histogram-based or covariance-based
            joint entropy measures

       mcwarp
            Multi-channel  nonrigid  B-spline  image  registration   using   histogram-based   or
            covariance-based joint entropy measures

       mip  Compute 2D Maximum Intensity Projection image from a 3D volume image along one of the
            coordinate directions

       mk_analyze_hdr
            Make header file according Analzye 7.5 format based on user-supplied  parameters  for
            geometry, data type, orientation, etc.

       mk_nifti_hdr
            Make header file according to NIFTI file format based on user-supplied parameters for
            geometry, data type, orientation, etc.

       mk_phantom_3d
            Generate 3D digital phantom images using a selection of drawing commands

       mrbias
            This program corrects intensity inhomogeneity artifacts in MR  images  using  a  bias
            field estimated via entropy minimization.

       overlap
            Compute overlap measures between two or more images

       probe
            This  tool  prints  pixel  values or symbolic labels at a list of user-provided image
            coordinates.

       reformatx
            Extended volume reformatter tool to compute reformatted images and Jacobian maps from
            arbitrary sequences of concatenated transformations

       registration
            This  program  performs  rigid  and  affine image registration using multi-resolution
            optimization of voxel-based image similarity measures.

       registrationx
            This program performs rigid and  affine  image  registration  using  multi-resolution
            optimization of voxel-based image similarity measures.

       regress
            Linear (and higher-order polynomial) regression of deformation fields and images.

       reorient
            Convert  between  image orientations, i.e., physically re-order pixel array and adapt
            stored anatomical orientation information

       sequence
            Analyze sequence of numerical values, which is read from standard input

       similarity
            Compute similarity measures such as intensity difference or  label  overlaps  between
            two images.

       split
            Split volume image into sub-images, i.e., to separate interleaved images into passes

       statistics
            Statistical  computations  on  image  pixel  intensities,  i.e.,  means  and standard
            deviations

       sympl
            Compute the approximate symmetry plane of an image to  determine,  for  example,  the
            mid-sagittal  plane  in  human  brain  images. Various forms of output are supported,
            e.g., writing the input image with the symmetry plane drawn into  it,  or  the  input
            image realigned along the symmetry plane.

       symplx
            Compute  the  approximate  symmetry  plane of an image to determine, for example, the
            mid-sagittal plane in human brain images. Various  forms  of  output  are  supported,
            e.g.,  writing  the  input  image with the symmetry plane drawn into it, or the input
            image realigned along the symmetry plane.

       ttest
            Pixelwise tests of statistical significance. Also compute correlations and z-scores

       unsplit
            Join separate image stacks into a single interleaved image volume

       volume_injection
            Reconstruction a high-resolution volume from multiple co-registered  (low-resolution)
            images using forward volume injection

       volume_reconstruction
            Iterative volume reconstruction from co-registered images using inverse interpolation
            or joint deblurring

       vtkxform
            An ASCII-format VTK file is read from standard input and a  user-provided  coordinate
            transformation  (optionally  inverted)  is  applied to the vertex coordinates.  A VTK
            file with transformed points is then written to standard output.

       warp This program performs nonrigid image registration using multi-resolution optimization
            of   voxel-based   image   similarity   measures   and  a  multi-resolution  B-spline
            transformation model.

       warp2ps
            Write deformation field as deformed grid in PostScript format for  visualization  and
            illustration

       warpx
            This program performs nonrigid image registration using multi-resolution optimization
            of  voxel-based  image  similarity   measures   and   a   multi-resolution   B-spline
            transformation model.

       xform2dfield
            Convert  parametric rigid or nonrigid transformation to deformation field, sampled at
            pixel locations of a given reference image

       xform2itk
            This tool converts coordinate transformations from CMTK format to ITK format and,  in
            the process, also correct for differences in image coordinate conventions

       xform2scalar
            This  tool  extracts  scalar  measures  from  transformations and deformation fields,
            sampled at grid locations, and writes the results to an image. Examples of  supported
            scalar  measures  are:  x,y,z  component  of  the  transformation,  magnitude  of the
            transformation, and Jacobian determinants.

AUTHORS

       Torsten Rohlfing, Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       From April 2009 through September 2011, CMTK Development and Maintenance was supported  by
       the  National  Institute  of  Biomedical  Imaging  and  Bioengineering  under Grant No.R01
       EB008381 (PI: Torsten Rohlfing).