Provided by: cmtk_3.0.0-1ubuntu1_amd64

**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. Seecmtk-<command>(1)manpage or output ofcmtk<command>--helpfor <command> specific options

**COMMANDS**

asegmentRegister 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_sri24Register 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_affineThis tool computes the average of a sequence of user-provided affine coordinate transformations.average_imagesThis tool computes pixelwiase average, variance, standard deviation, z-score, or entropy images from a list of user-provided intensity images.average_labelsAverage co-registered label images using partial volumesavg_admCompute average-shape average-intensity images and deformation maps using an active deformation model.concat_affineThis tool computes the explicit concatenation of multiple affine coordinate transformations, each of which can be optionally inverted.convert_warpThis tool converts nonrigid B-spline free-format deformation coordinate transformations between different representations (e.g., absolute vs. relative vectors). Also creates fractional transformations.convertxThis 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.dbtoolThis tool modifies and queries the database of images and transformations between them.dcm2imageCombine sets of DICOM slices to 3D image stacksdescribeThis tool prints a detailed description of the input files as either image(s) or transformation(s).destripeThis program corrects stripe artifacts in acquired image stacks which can result from between-slice intensity scale differences.detect_adni_phantomThis 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_filterThis tool detects spherical objects in three-dimensional images.dof2matConvert affine transformation from degrees-of-freedom representation to matrix formdwi_mask_bad_slicesThis 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.epiunwarpCorrect B0 field inhomogeneity-induced distortion in Echo Planar Images (e.g., diffusion-weighted images) using two images acquired with opposing phase encoding directions.fib2imageFiber 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.fibxformA 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.filmThis tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected imagefilterThis tool applies spatial filtering operators, including cnotent-sensitive opersators, based on selective Gaussian kernels.fit_affine_dfieldFit a linear affine transformation to a nonrigid transformation, either a B-spline free-form deformation or a non-parametric deformation field.fit_affine_xformFit a linear affine transformation to a list of concatenated, optionally inverted, transformations.fit_affine_xform_landmarksFit a linear affine transformation to a set of matched landmarks.fit_spline_dfieldFit a parametric nonrigid transformation (B-spline free-form deformation) to a deformation fieldfit_spline_xformFit a parametric nonrigid transformation (B-spline free-form deformation) to a list of concatenated, optionally inverted, transformations.fviewglmStatistical modeling of pixel intensities in multiple images using a General Linear Model.gmmSegment an image into c classes using the EM algorithm for Gaussian mixtures with optional priors.gregxformTHIS TOOL IS DEPRECATED. PLEASE USE streamxform INSTEAD.groupwise_affineThis 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_initCompute initial affine alignment for a group of input images, which can be used as an input for groupwise registrationgroupwise_warpThis 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').hausdorffThis tool computes the Hausdorff distance between two label images.histogramCreate a histogram of image intensities and write as tab-separated text file to standard outputimagemathPerform operations on images using stack-based postfix notation.interleaved_bad_slicesThis tool reads a time series of 3D images and detects outliers.iterative_shape_averagingjidbThis tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected imagelevelsetLevelset-type segmentation of foreground/background using minimum regional variance energylmsbaThis tool combines multiple multi-class segmentations from co-registered and reformatted atlases using locally-weighted Shape-Based Averaging.lsbaThis tool combines multiple binary segmentations from co-registered and reformatted atlases using locally-weighted Shape-Based Averaging.lvoteThis tool combines multiple segmentations fro co-registered and reformatted atlases using locally-weighted voting.make_initial_affineCompute initial affine transformation by aligning centers of mass or principal axesmat2dofConvert transformation matrix to degrees of freedommcaffineMulti-channel affine image registration using histogram-based or covariance-based joint entropy measuresmcwarpMulti-channel nonrigid B-spline image registration using histogram-based or covariance-based joint entropy measuresmk_adni_phantomGenerate image of the ADNI structural imaging calibration phantom (a.k.a. Magphan EMR051).mk_analyze_hdrMake header file according Analzye 7.5 format based on user-supplied parameters for geometry, data type, orientation, etc.mk_nifti_hdrMake header file according to NIFTI file format based on user-supplied parameters for geometry, data type, orientation, etc.mk_phantom_3dGenerate 3D digital phantom images using a selection of drawing commandsmrbiasThis program corrects intensity inhomogeneity artifacts in MR images using a bias field estimated via entropy minimization.overlapCompute overlap measures between two or more imagesprobeThis tool prints pixel values or symbolic labels at a list of user-provided image coordinates.pxsearchThis 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.reformatxExtended volume reformatter tool to compute reformatted images and Jacobian maps from arbitrary sequences of concatenated transformationsregistrationThis program performs rigid and affine image registration using multi-resolution optimization of voxel-based image similarity measures.registrationxThis program performs rigid and affine image registration using multi-resolution optimization of voxel-based image similarity measures.regressLinear (and higher-order polynomial) regression of deformation fields and images.reorientConvert between image orientations, i.e., physically re-order pixel array and adapt stored anatomical orientation informationsbaAverage 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.sbaiAverage 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.sequenceAnalyze sequence of numerical values, which is read from standard inputsh_command_line_parsersimilarityCompute similarity measures such as intensity difference or label overlaps between two images.splitSplit volume image into sub-images, i.e., to separate interleaved images into passesstatisticsStatistical computations on image pixel intensities, i.e., means and standard deviationsstream_pixelsThis 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.streamxformAn 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.symplCompute 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.symplxCompute 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.ttestPixelwise tests of statistical significance. Also compute correlations and z-scoresunsplitJoin separate image stacks into a single interleaved image volumeunwarp_image_phantomThis 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.vol2csvThis 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_injectionReconstruction a high-resolution volume from multiple co-registered (low-resolution) images using forward volume injectionvolume_reconstructionIterative volume reconstruction from co-registered images using inverse interpolation or joint deblurringvtkxformAn 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.warpThis program performs nonrigid image registration using multi-resolution optimization of voxel-based image similarity measures and a multi-resolution B-spline transformation model.warp2psWrite deformation field as deformed grid in PostScript format for visualization and illustrationwarpxThis program performs nonrigid image registration using multi-resolution optimization of voxel-based image similarity measures and a multi-resolution B-spline transformation model.xform2dfieldConvert parametric rigid or nonrigid transformation to deformation field, sampled at pixel locations of a given reference imagexform2itkThis tool converts coordinate transformations from CMTK format to ITK format and, in the process, also correct for differences in image coordinate conventionsxform2scalarThis 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.