Man Pages in cmtk

Section 1: Executable programs or shell commands

cmtk.1

The computational morphometry toolkit

cmtk-asegment.1

Atlas-based segmentation

cmtk-asegment_sri24.1

Segmentation using sri24 atlas

cmtk-average_affine.1

Average affine transformations

cmtk-average_images.1

Average images

cmtk-average_labels.1

Label image averaging

cmtk-avg_adm.1

Average using adm

cmtk-concat_affine.1

Concatenate affine transformations

cmtk-convert_warp.1

Convert nonrigd transformations.

cmtk-convertx.1

Convert between image file formats and data types.

cmtk-dbtool.1

Image/transformation database maintenance and query tool

cmtk-dcm2image.1

Dicom to image

cmtk-describe.1

Describe image and transformation file formats and parameters

cmtk-destripe.1

Destripe volume image data.

cmtk-detect_adni_phantom.1

Detect adni phantom landmarks in phantom image

cmtk-detect_spheres_matched_filter.1

Detect spheres

cmtk-dof2mat.1

Degrees of freedom to matrix

cmtk-dwi_mask_bad_slices.1

Find bad slices in set of diffusion-weighted images.

cmtk-epiunwarp.1

Unwarp echo planar images

cmtk-fib2image.1

Draw image from point coordinates of fiber tracks from .fib file.

cmtk-fibxform.1

Apply coordinate transformations to point coordinates in .fib file.

cmtk-film.1

Fix interleaved motion using inverse interpolation

cmtk-filter.1

Filter a volume image

cmtk-fit_affine_dfield.1

Fit affine transformation to nonrigid transformation

cmtk-fit_affine_xform.1

Fit single affine transformation to concatenated list

cmtk-fit_affine_xform_landmarks.1

Fit affine transformation to landmarks

cmtk-fit_spline_dfield.1

Deformation field to transformation

cmtk-fit_spline_xform.1

Fit single b-spline transformation to concatenated transformation list

cmtk-fview.1

Fusion viewer.

cmtk-geomatch.1

Check whether the geometries (e.g., grid dimensions, pixel sizes, spatial coordinates) or two or more images match.

cmtk-glm.1

General linear model

cmtk-gmm.1

Gaussian mixture model segmentation

cmtk-gregxform.1

Apply coordinate transformations to lists of point coordinates

cmtk-groupwise_affine.1

Affine population registration

cmtk-groupwise_init.1

Affine initialization for groupwise registration

cmtk-groupwise_warp.1

Nonrigid population registration

cmtk-hausdorff.1

Hausdorff distance.

cmtk-histogram.1

Image histogram

cmtk-imagemath.1

Image operations

cmtk-interleaved_bad_slices.1

Find bad slices in a time series of interleaved images (e.g., a resting-state fmri series).

cmtk-jidb.1

Fix interleaved motion using joint iterative deblurring

cmtk-levelset.1

Levelset segmentation

cmtk-lmsba.1

Local voting.

cmtk-lsba.1

Local voting.

cmtk-lvote.1

Local voting.

cmtk-make_initial_affine.1

Initialize affine transformation

cmtk-mat2dof.1

Matrix to degrees of freedom

cmtk-mcaffine.1

Multi-channel affine registration

cmtk-mcwarp.1

Multi-channel nonrigid registration

cmtk-mk_adni_phantom.1

Generate adni phantom image

cmtk-mk_analyze_hdr.1

Make analyze header file

cmtk-mk_nifti_hdr.1

Make nifti header file

cmtk-mk_phantom_3d.1

Generate phantom image

cmtk-mrbias.1

Mr image intensity bias field correction

cmtk-overlap.1

Overlap computation

cmtk-probe.1

Probe image data.

cmtk-pxsearch.1

Search image neighborhoods for pixels.

cmtk-reformatx.1

Volume reformatter

cmtk-registration.1

Rigid and affine registration

cmtk-registrationx.1

Rigid and affine registration

cmtk-regress.1

Regression

cmtk-reorient.1

Reorientation

cmtk-sba.1

Shape-based averaging of label images

cmtk-sbai.1

Shape-based averaging and interpolation of label images

cmtk-sequence.1

Value sequence

cmtk-similarity.1

Image similarity

cmtk-split.1

Split images

cmtk-statistics.1

Image statistics

cmtk-stream_pixels.1

Stream pixel data from one or more images to standard output.

cmtk-streamxform.1

Apply coordinate transformation to point coordinates from text stream.

cmtk-sympl.1

Symmetry plane computation

cmtk-symplx.1

Symmetry plane computation

cmtk-ttest.1

T-tests

cmtk-unsplit.1

Unsplit images

cmtk-unwarp_image_phantom.1

Create transformation to unwarp an image based on a phantom description

cmtk-vol2csv.1

Compute regional volumes and write to csv file.

cmtk-volume_injection.1

Volume injection

cmtk-volume_reconstruction.1

Volume reconstruction

cmtk-vtkxform.1

Apply coordinate transformation to point coordinates in vtk file.

cmtk-warp.1

B-spline nonrigid registration

cmtk-warp2ps.1

Deformation to postscript

cmtk-warpx.1

B-spline nonrigid registration

cmtk-xform2dfield.1

Transformation to deformation field

cmtk-xform2itk.1

Convert affine transformations to itk format.

cmtk-xform2scalar.1

Extract scalar measures from transformations and deformation fields