cmtk - Online in the Cloud

PROGRAM:

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

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

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