Provided by: cmtk_2.1.0-1_amd64
cmtk - the Computational Morphometry Toolkit
cmtk <command> [options]
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
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.
Torsten Rohlfing, Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff
Report bugs at http://nitrc.org/projects/cmtk/
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).