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

geomatch

This tool reads two or more images and tests whether their grid dimensions, pixel sizes, and image-to-space transformations match. Optionally, all images are reoriented into standard orientation before performing the test. If all images match, the tool returns with exit code 0, otherwise it returns with exit code 2. In case of an error (e.g., one of the images can not be read), the exit code is 1.

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

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 either a polynomial transformation or 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

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.