Provided by: cmtk_3.0.0-1ubuntu1_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 human  brain  atlas,  then
            reformat one of the atlas label maps to the target image. Note: it is assume that the
            target image is skull-stripped, i.e., contains only the brain.

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

       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   B-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  files  as  either  image(s)  or
            transformation(s).

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

       detect_adni_phantom
            This tool detects the locations of all spherical landmarks  in  a  3D  image  of  the
            Magphan EMR051 structural imaging phantom (a.k.a. ADNI Phantom).

       detect_spheres_matched_filter
            This tool detects spherical objects in three-dimensional images.

       dof2mat
            Convert affine transformation from degrees-of-freedom representation to matrix form

       dwi_mask_bad_slices
            This  tool reads a set of 3D diffusion-weighted MR images and finds bad slices. A bad
            slice in a diffusion image is detected as one  whose  mean  intensity  is  outside  a
            specified  interval around the mean of the means of all corresponding slices from the
            remaining diffusion images.

       epiunwarp
            Correct B0 field  inhomogeneity-induced  distortion  in  Echo  Planar  Images  (e.g.,
            diffusion-weighted  images)  using  two  images acquired with opposing phase encoding
            directions.

       fib2image
            Fiber tracking results from the UNC Fiber Tracking tool are read from Standard  Input
            and  all  fiber points are drawn into a 3D image. The result is written in one of the
            supported image file formats.

       fibxform
            A file with fiber tracking results from the UNC Fiber  Tracking  tool  is  read  from
            Standard  Input and one or more (concatenated) coordinate transformations are applied
            to all fiber point coordinates. The result is written to Standard  Output,  again  in
            UNC fiber file format.

       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.

       fit_affine_dfield
            Fit  a  linear  affine transformation to a nonrigid transformation, either a B-spline
            free-form deformation or a non-parametric deformation field.

       fit_affine_xform
            Fit a linear affine transformation to a list of  concatenated,  optionally  inverted,
            transformations.

       fit_affine_xform_landmarks
            Fit a linear affine transformation to a set of matched landmarks.

       fit_spline_dfield
            Fit  a  parametric  nonrigid  transformation  (B-spline  free-form  deformation) to a
            deformation field

       fit_spline_xform
            Fit a parametric nonrigid transformation (B-spline free-form deformation) to  a  list
            of concatenated, optionally inverted, transformations.

       fview

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

       gmm  Segment an image into c classes using the EM algorithm  for  Gaussian  mixtures  with
            optional priors.

       gregxform
            THIS TOOL IS DEPRECATED. PLEASE USE streamxform INSTEAD.

       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.

       interleaved_bad_slices
            This tool reads a time series of 3D images and detects outliers.

       iterative_shape_averaging

       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

       lmsba
            This   tool  combines  multiple  multi-class  segmentations  from  co-registered  and
            reformatted atlases using locally-weighted Shape-Based Averaging.

       lsba This tool combines multiple binary segmentations from co-registered  and  reformatted
            atlases using locally-weighted Shape-Based Averaging.

       lvote
            This  tool  combines multiple segmentations fro co-registered and reformatted atlases
            using locally-weighted voting.

       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

       mk_adni_phantom
            Generate image of the ADNI structural imaging  calibration  phantom  (a.k.a.  Magphan
            EMR051).

       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.

       pxsearch
            This  tool  reads an image file, as well as a list of pixel coordinates from standard
            input. For each pixel, a local neighbourhood   in  the  image  is  searched  for  the
            maximum value. The location of the maximum is then written to standard output.

       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

       sba  Average  segmentations  (label  fields)  using  the Euclidean Distance Transform. All
            input images must be in the same space. EDT is  computed  in  this  space  also.  See
            http://dx.doi.org/10.1109/TIP.2006.884936 for details of the underlying algorithm.

       sbai Average  segmentations  (label  fields)  using the Euclidean Distance Transform. This
            tool performs joint interpolation and averaging by interpolating from the  EDT.  This
            requires that the inputs are transformations from the same fixed to (not necessarily)
            different moving images. EDT computation is done in the space of each  moving  image.
            See   http://dx.doi.org/10.1109/TIP.2006.884936   for   details   of  the  underlying
            algorithm.

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

       sh_command_line_parser

       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

       stream_pixels
            This tool reads one or more images and writes all their pixels to standard output  in
            binary  form.  Optionally,  each  image  can  be reoriented to a specified anatomical
            orientation and/or converted to a different data type.  This  is  useful  for  piping
            image data through a pipeline, e.g., the Camino DTI toolkit.

       streamxform
            An  ASCII-format  list  of  point coordinates is read from standard input and a user-
            provided sequence of coordinate transformations (each optionally inverted) is applied
            to them. The transformed points are then written to standard output.

       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

       unwarp_image_phantom
            This  tool  computes  a   B-spline  free-form  deformation  to  unwarp  an image. The
            transformation is based  on  expected  and  detected  landmarks  in  an  image  of  a
            structural  phantom  acquired on the same scanner. Use the 'detect_adni_phantom' tool
            to detect landmarks  of  the  ADNI  Phantom  in  an  image  and  generate  a  phantom
            description file suitable for use with this tool.

       vol2csv
            This  tool  computes  the  volumes of regions in a label image. It optionally accepts
            density maps (e.g., for different tissues) and computes  and  prints  the  per-region
            content for each. Also, the tool can accept an optional 'pixel volume' map to account
            for local pixel volume variations, e.g., due to spatial distortion.

       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, 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.