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<div class="section" id="applications">
<span id="id1"></span><h1>Applications<a class="headerlink" href="#applications" title="Permalink to this headline">¶</a></h1>
<div class="section" id="commands">
<span id="commandssummary"></span><h2>Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h2>
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<table border="1" class="docutils">
<colgroup>
<col width="38%" />
<col width="62%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Command</th>
<th class="head">Description</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td><a class="reference internal" href="commands/aggregate-images.html"><span class="doc">aggregate-images</span></a></td>
<td>Aggregates multiple (co-registered) input images into a single output image
or report statistics thereof within a specified region of interest.
The input images have to be defined in the same discrete finite image space.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/average-dofs.html"><span class="doc">average-dofs</span></a></td>
<td>This command averages a number of input transformations.
It can be used to construct a brain image atlas and has been
utilized for the construction of the spatio-temporal fetal/neonatal
brain atlases available at <a class="reference external" href="http://brain-development.org/brain-atlases/">http://brain-development.org/brain-atlases/</a>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/average-images.html"><span class="doc">average-images</span></a></td>
<td>Computes voxel-wise average image of the given (transformed) input images.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/average-measure.html"><span class="doc">average-measure</span></a></td>
<td>Average voxel-wise measure within each region of interest (ROI).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/average-overlap.html"><span class="doc">average-overlap</span></a></td>
<td>No description available.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/bisect-dof.html"><span class="doc">bisect-dof</span></a></td>
<td>This command bisects a rigid or affine transformation by calculating the
matrix square root of the transformation matrix.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/blend-surface.html"><span class="doc">blend-surface</span></a></td>
<td>Blends two surface meshes with index based one-to-one point correspondences
by taking the point coordinates for selected points from the first surface
mesh and all others from the second surface mesh. Points at the boundary of
the point selection mask are blended between the two mesh positions of the
corresponding points. For other points, i.e., those further away from the
boundary, the blending factor is either 0 or 1.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-boundary-map.html"><span class="doc">calculate-boundary-map</span></a></td>
<td>Compute a surface boundary map suitable for the computation of a
surface map to a 2D primitive shape such as a disk, square, or polygon.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-distance-map.html"><span class="doc">calculate-distance-map</span></a></td>
<td>Computes distance transformation of binary object mask.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-element-wise.html"><span class="doc">calculate-element-wise</span></a></td>
<td>This tool can be used for basic calculations from a sequence of data values read
either from an image or a VTK pointset. It can be used, for example, to add two
data sequences and to divide the result by a constant. The current sequence can
be written to an output file again using <a class="reference internal" href="commands/calculate-element-wise.html#cmdoption-calculate-element-wise-out"><code class="xref std std-option docutils literal"><span class="pre">calculate-element-wise</span> <span class="pre">-out</span></code></a>. Additionally, statistics
of the current data sequence can be computed such as the mean or variance.
The order of the data transformations and calculation of statistics is determined
by the order of the command-line arguments.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-exponential-map.html"><span class="doc">calculate-exponential-map</span></a></td>
<td>Reads a dense 3D (2D) stationary velocity field, computes the corresponding
dense 3D (2D) displacement field, and writes the resulting vector field.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-filtering.html"><span class="doc">calculate-filtering</span></a></td>
<td>Calculates statistics by filtering with a kernel.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-gradients.html"><span class="doc">calculate-gradients</span></a></td>
<td>A blur with S.D. sigma is appled before the gradient is estimated</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-lie-bracket.html"><span class="doc">calculate-lie-bracket</span></a></td>
<td>Computes the Lie bracket of two vector fiels <span class="math">\(z = [x, y]\)</span>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-logarithmic-map.html"><span class="doc">calculate-logarithmic-map</span></a></td>
<td>Reads a dense 3D (2D) displacement field, computes the corresponding
stationary 3D (2D) velocity field, and writes the resulting vector field.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-surface-attributes.html"><span class="doc">calculate-surface-attributes</span></a></td>
<td>Calculate attributes of input surface such as normals and curvature.
If required, as in case of the curvature calculations, the input mesh
is triangulated beforehand if it contains non-triangular faces.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-surface-map.html"><span class="doc">calculate-surface-map</span></a></td>
<td>This tool computes a mapping for each point on the surface of a given input shape
embedded in 3D space. The output is a (piecewise linear) function which assigns each
point on the surface of the input shape one or more values. In case of non-closed surfaces,
the output map can interpolate any values given on the boundary of the surface at the
interior points of the surface. More common use cases are to compute a bijective mapping
from one geometric shape to another geometric shape with identical topology. The resulting
map is a parameterization of the surface of the input shape. Such parameterization can be
used for texturing, object morphing, and surface registration.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/calculate-surface-spectrum.html"><span class="doc">calculate-surface-spectrum</span></a></td>
<td>Performs a spectral analysis of the general graph Laplacian matrix
computed from the given input surface mesh(es).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/calculate-volume-map.html"><span class="doc">calculate-volume-map</span></a></td>
<td>This tool computes a mapping for each point of the volume of a given input point set.
The input is either a piecewise linear complex (PLC), i.e., a tesselation of the surface,
or a tesselation of the shape’s volume such as a tetrahedral mesh generated from a PLC.
The output is a volumetric map which assigns points of the volume one or more values.
The volumetric map can in general interpolate any values given on the surface of the map
domain at the interior of the volume. More common use cases are to compute a bijective
map from one volumetric shape to another with identical topology. The resulting map is a
re-parameterization of the volume of the input shape. Such parameterization can be used for
texturing, object deformation (cf. “cage deformation”), object morphing, and surface-
constraint image registration.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/change-label.html"><span class="doc">change-label</span></a></td>
<td>Changes the labels of the <init_labels> image inside the <mask> image
according to probability maps <probmap_1> .. <probmap_N> with labels <label_1> .. <label_N> respectively and saves the result in <output></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/close-image.html"><span class="doc">close-image</span></a></td>
<td>Closes holes by first dilating and then eroding an input image.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/close-scalars.html"><span class="doc">close-scalars</span></a></td>
<td>Closes scalar data of an input point set by perfoming a dilation
followed by the same number of erosions. When the input data array
has more than one component, each component is processed separately.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/combine-images.html"><span class="doc">combine-images</span></a></td>
<td>Concatenate two or more either 2D images to form a 3D volume,
or 3D volumes to form a 3D+t temporal sequence. All input images
must have the same image attributes, except in either the third (2D)
or the third and fourth (3D) image dimension.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/compose-dofs.html"><span class="doc">compose-dofs</span></a></td>
<td>Computes the composition T of the given input transformations such that</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/compose-maps.html"><span class="doc">compose-maps</span></a></td>
<td>Computes the composition g of the given input maps such that</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/construct-atlas.html"><span class="doc">construct-atlas</span></a></td>
<td>Construct (spatio-temporal) atlas from images of the same anatomy of different
subjects. To construct a spatio-temporal atlas, images of subjects at
different ages spread over the atlas time range are required. Please cite the
following preprint when you use this command in your research (or the
respective peer-reviewed article when accepted): Schuh et al., “Unbiased
construction of a temporally consistent morphological atlas of neonatal brain
development”, bioRxiv, 2018. doi:10.1101/251512</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/convert-dof.html"><span class="doc">convert-dof</span></a></td>
<td>Converts between different transformation file formats:</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/convert-image.html"><span class="doc">convert-image</span></a></td>
<td>Converts an image from one voxel type to another.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/convert-pointset.html"><span class="doc">convert-pointset</span></a></td>
<td>Convert point set from one (file) format to another.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/copy-pointset-attributes.html"><span class="doc">copy-pointset-attributes</span></a></td>
<td>Copies point and/or cell data from a source point set to a target point set
and writes the resulting amended point set to the specified output file.
When no separate output file is specified, the target point set is overwritten.
This command can also convert from point data to cell data and vice versa.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/cut-brain.html"><span class="doc">cut-brain</span></a></td>
<td>Cut input brain volume/mask into left and/or right hemisphere(s).</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/decimate-surface.html"><span class="doc">decimate-surface</span></a></td>
<td>Decimates a (triangular) mesh using VTK’s <code class="docutils literal"><span class="pre">vtkQuadricDecimation</span></code> filter.
In case of <a class="reference internal" href="commands/decimate-surface.html#cmdoption-decimate-surface-pro"><code class="xref std std-option docutils literal"><span class="pre">decimate-surface</span> <span class="pre">-pro</span></code></a>, the <code class="docutils literal"><span class="pre">vtkDecimatePro</span></code> filter is used instead.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/deform-mesh.html"><span class="doc">deform-mesh</span></a></td>
<td>Iteratively minimizes a deformable surface model energy functional. The gradient of
the energy terms are the internal and external forces of the deformable surface model.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/delete-pointset-attributes.html"><span class="doc">delete-pointset-attributes</span></a></td>
<td>Delete point data and/or cell data from input point set.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/detect-edges.html"><span class="doc">detect-edges</span></a></td>
<td>Convolves the input image with an edge detection operator.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/dilate-image.html"><span class="doc">dilate-image</span></a></td>
<td>Dilates an input image by replacing a voxel’s value by the maximum
of the values of its neighboring voxels.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/dilate-scalars.html"><span class="doc">dilate-scalars</span></a></td>
<td>Dilates scalar data of an input point set by replacing a value by the
maximum of the adjacent data values. When the input data array has
more than one component, each component is processed separately.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/downsample-image.html"><span class="doc">downsample-image</span></a></td>
<td>Downsamples an image using an iterative Gaussian pyramid filter.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/draw-em.html"><span class="doc">draw-em</span></a></td>
<td>Runs the DrawEM segmentation at the input image with the provided N probability maps of structures.
The main algorithm is outlined in [1].</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/edit-dof.html"><span class="doc">edit-dof</span></a></td>
<td>This tool provides a generic way of modifying the parameters of a
transformation (linear as well as non-linear). It uses the generic
interface member function Transformation::Set whose arguments
are the name of the parameter and the value to be set as string.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/edit-image.html"><span class="doc">edit-image</span></a></td>
<td>Modifies the attributes of an image stored in the header.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/em.html"><span class="doc">em</span></a></td>
<td>Runs EM segmentation at the input image with the provided N probability maps of structures.
e.g. em input.nii.gz 5 bg.nii.gz csf.nii.gz gm.nii.gz wm.nii.gz dgm.nii.gz segmentation.nii.gz</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/em-hard-segmentation.html"><span class="doc">em-hard-segmentation</span></a></td>
<td>Computes the hard segmentation of the N atlases.
Optionally MRF smoothing can be additionally applied.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/erode-image.html"><span class="doc">erode-image</span></a></td>
<td>Erodes an input image by replacing a voxel’s value by the minimum
of the values of its neighboring voxels.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/erode-scalars.html"><span class="doc">erode-scalars</span></a></td>
<td>Erodes scalar data of an input point set by replacing a value by the
minimum of the adjacent data values. When the input data array has
more than one component, each component is processed separately.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-atlas.html"><span class="doc">evaluate-atlas</span></a></td>
<td>Evaluate (spatio-temporal) atlas sharpness measures.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-cardiac-motion.html"><span class="doc">evaluate-cardiac-motion</span></a></td>
<td>Evaluate cardiac motion. This command computes the displacement or strain
at each vertex on a myocardial surface mesh.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-distance.html"><span class="doc">evaluate-distance</span></a></td>
<td>Evaluate distance between two given point sets. With increased verbosity (see <a class="reference internal" href="commands/evaluate-distance.html#cmdoption-evaluate-distance-v"><code class="xref std std-option docutils literal"><span class="pre">evaluate-distance</span> <span class="pre">-v</span></code></a>),
the mean and standard deviation of the measured distances (verbosity level >=1) and the
individual distance for each target point is reported (verbosity level >=2).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-distortion.html"><span class="doc">evaluate-distortion</span></a></td>
<td>Computes the distortion of a surface mesh under deformation, when
mapped to the surface of another solid with equivalent topology, or
flattened to the plane or sphere, respectively.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-dof.html"><span class="doc">evaluate-dof</span></a></td>
<td>Calculates registration transformation quality measures such as the voxel-wise
cumulative or mean inverse-consistency error (CICE/MICE) for pairs of forward
transformation from target to source and backward transformation from source
to target image. Another voxel-wise measure that can be computed using this
program are the cumulative or mean transitivity error (CTE/MTE) given three
transformations, from target (A) to B, from B to C, and from C to A again.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-jacobian.html"><span class="doc">evaluate-jacobian</span></a></td>
<td>Computes the Jacobian determinant of the given transformation at
each target image voxel. If no <output> image name is given,
the statistics of the Jacobian determinant distribution are printed
to STDOUT instead, such as min, max, and mean.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-overlap.html"><span class="doc">evaluate-overlap</span></a></td>
<td>Computes the overlap of either two intensity images (average SI)
or two segmentations (see <a class="reference internal" href="commands/evaluate-overlap.html#cmdoption-evaluate-overlap-label"><code class="xref std std-option docutils literal"><span class="pre">evaluate-overlap</span> <span class="pre">-label</span></code></a>). If more than one source image
is given, the overlap between each of these and the target is evaluated.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-similarity.html"><span class="doc">evaluate-similarity</span></a></td>
<td>Evaluates the (dis-)similarity of two intensity images.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-surface-map.html"><span class="doc">evaluate-surface-map</span></a></td>
<td>Evaluates quantitative quality measures of a surface map.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-surface-mesh.html"><span class="doc">evaluate-surface-mesh</span></a></td>
<td>Prints surface mesh quality measures and topology information.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/evaluate-surface-overlap.html"><span class="doc">evaluate-surface-overlap</span></a></td>
<td>Reports label statistics given two surface meshes and a text file
listing the indices of corresponding points. The labels have to be
stored as named point data array in both datasets.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/evaluate-volume-map.html"><span class="doc">evaluate-volume-map</span></a></td>
<td>Evaluates quantitative measures of a surface map or volumetric map
such as its harmonic energy.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/extract-connected-components.html"><span class="doc">extract-connected-components</span></a></td>
<td>Extracts connected components from input segmentation label image.
By default, the largest connected component is extracted.
In case of <a class="reference internal" href="commands/extract-connected-components.html#cmdoption-extract-connected-components-output-component-labels"><code class="xref std std-option docutils literal"><span class="pre">extract-connected-components</span> <span class="pre">-output-component-labels</span></code></a>, the labels
of the components are written instead.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/extract-connected-points.html"><span class="doc">extract-connected-points</span></a></td>
<td>Extract (largest) connected components of the input point set.
The connected components are sorted by size, where the largest
connected component has index 0.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/extract-image-region.html"><span class="doc">extract-image-region</span></a></td>
<td>Crop/pad image by extracting a region of interest and optionally split the extracted region into separate image files, e.g., individual slices of a volume saved as individual image files. The output image region
is chosen such that it contains the union of all specified axis-aligned
rectangular input image regions. In case of <a class="reference internal" href="commands/extract-image-region.html#cmdoption-extract-image-region-pad"><code class="xref std std-option docutils literal"><span class="pre">extract-image-region</span> <span class="pre">-pad</span></code></a>, the output
region does not have to be fully contained within the input image.
Values outside are then set to the specified padding value.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/extract-image-slice.html"><span class="doc">extract-image-slice</span></a></td>
<td>No description available.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/extract-image-volume.html"><span class="doc">extract-image-volume</span></a></td>
<td>No description available.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/extract-pointset-cells.html"><span class="doc">extract-pointset-cells</span></a></td>
<td>Extract point set/surface elements which meet the specified criteria.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/extract-pointset-surface.html"><span class="doc">extract-pointset-surface</span></a></td>
<td>Extract surface of point set. If more than one input point set is given,
it computes the boundary of the union, intersection, or difference volume
computed from the volumes defined by the individual input surfaces.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/extract-surface.html"><span class="doc">extract-surface</span></a></td>
<td>Extract the isosurface from an intensity image or segmentation.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/fill-holes.html"><span class="doc">fill-holes</span></a></td>
<td>Fills holes in the input.
Note: The code is adapted from fslmaths -fillh</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/fill-holes-nn-based.html"><span class="doc">fill-holes-nn-based</span></a></td>
<td>Fills holes in the input.
The surrounding voxels of the suspected-holes are measured and if the majority belongs to the input they are filled.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/flip-image.html"><span class="doc">flip-image</span></a></td>
<td>Swaps the two image dimensions at a time, in the order of the input
options. Both, the image data and the coordinates of the image origin
are swapped each time an input option is processed. To swap the image
axes instead of the origin, use the <a class="reference internal" href="commands/flip-image.html#cmdoption-flip-image-axes"><code class="xref std std-option docutils literal"><span class="pre">flip-image</span> <span class="pre">-axes</span></code></a> option before the
swap options. This option should be used to reorder the image dimensions
without changing the world coordinates of the voxels. When swapping of
the coordinate axes is enabled, the coordinates of the image origin are
kept the same, i.e., <a class="reference internal" href="commands/flip-image.html#cmdoption-flip-image-origin"><code class="xref std std-option docutils literal"><span class="pre">flip-image</span> <span class="pre">-origin</span></code></a> is ignored. The default behavior
is to swap the image data and the coordinates of the image origin. This
may in many cases not have the desired effect, but has been this way
already for some time.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/help-rst.html"><span class="doc">help-rst</span></a></td>
<td>No description available.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/info.html"><span class="doc">info</span></a></td>
<td>Prints some useful information about the given input file, which
can be an image, transformation (requires MIRTK Transformation module),
or point set (requires MIRTK Point Set module).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/init-dof.html"><span class="doc">init-dof</span></a></td>
<td>This tool either creates a new affine transformation with the given parameters
or approximates an affine transformation or non-rigid deformation given
a set of corresponding landmarks or point displacements (see <a class="reference internal" href="commands/init-dof.html#cmdoption-init-dof-displacements"><code class="xref std std-option docutils literal"><span class="pre">init-dof</span> <span class="pre">-displacements</span></code></a>).</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/invert-dof.html"><span class="doc">invert-dof</span></a></td>
<td>Inverts any transformation. In case of a non-rigid transformation
the output transformation only approximates the true inverse.
When the inverse mapping is not defined at a given point, the
output transformation at this point depends on the interpolation
numerical approximate solution found.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/kmeans.html"><span class="doc">kmeans</span></a></td>
<td>Runs k-means clustering at the input image with the provided K number of classes.
e.g. kmeans input.nii.gz 10 output.nii.gz</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/match-histogram.html"><span class="doc">match-histogram</span></a></td>
<td>Matches the intensity distribution of the source image to match the
distribution of the target image using a piecewise linear function [1].</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/match-points.html"><span class="doc">match-points</span></a></td>
<td>Writes for each point in a target point set its corresponding point in
the source point set. The found correspondences can be either written
to an output point set with indices and difference vectors stored as
point data, or a text file listing for each target point index the
index of the corresponding source point.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/measure-volume.html"><span class="doc">measure-volume</span></a></td>
<td>Measures the volume of each label in the input image</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/merge-surfaces.html"><span class="doc">merge-surfaces</span></a></td>
<td>Merge surface meshes at segmentation label boundaries. The input
surfaces must follow closely the boundary of a segment in the given
image segmentation. Two surfaces are then merged at the longest
common intersection boundary. When the two surfaces share no such
segmentation boundary, the surfaces are not connected.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/normalize.html"><span class="doc">normalize</span></a></td>
<td>Normalizes the intensity distribution of an image to be similar to
the intensity distribution of a given reference image. Moreover,
this tool can be used to equalize the histograms of either a single
given image or two images using the same transfer function.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/offset-surface.html"><span class="doc">offset-surface</span></a></td>
<td>Displaces surface mesh points by a given amount along the surface normal
to create an offset surface mesh. To prevent self-intersections, a dense
offset surface can optionally first be sampled from an implicit offset
surface model onto which each point of the input surface is projected.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/open-image.html"><span class="doc">open-image</span></a></td>
<td>Removes small connections between objects by first eroding and then
dilating an input image.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/open-scalars.html"><span class="doc">open-scalars</span></a></td>
<td>Opens scalar data of an input point set by perfoming an erosion
followed by the same number of dilations. When the input data array
has more than one component, each component is processed separately.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/project-onto-surface.html"><span class="doc">project-onto-surface</span></a></td>
<td>Assign scalars or labels to either the vertices or the cells of a surface mesh.
When the input is a real-valued image, the values are linearly interpolated.
When the input is a segmentation image, the value assigned to a vertex/cell is the
label of the nearest voxel in the given segmentation image. For the projection of
cortical labels onto the WM/GM or GM/CSF boundary, use <a class="reference internal" href="commands/project-onto-surface.html#cmdoption-project-onto-surface-white"><code class="xref std std-option docutils literal"><span class="pre">project-onto-surface</span> <span class="pre">-white</span></code></a> or <a class="reference internal" href="commands/project-onto-surface.html#cmdoption-project-onto-surface-pial"><code class="xref std std-option docutils literal"><span class="pre">project-onto-surface</span> <span class="pre">-pial</span></code></a>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/recon-neonatal-cortex.html"><span class="doc">recon-neonatal-cortex</span></a></td>
<td>Reconstruct neonatal cortex from MR brain scan and Draw-EM segmentation</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/reflect-image.html"><span class="doc">reflect-image</span></a></td>
<td>Applies a one or more spatial reflections along an image axis.
A more generic tool that can also be used to swap two axes is
the flip-image command.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/register.html"><span class="doc">register</span></a></td>
<td>Registers a set of images, polygonal surface meshes, and/or point clouds (e.g. fiducial markers).
The set of input images can be comprised of multiple channels (e.g., acquired with different imaging
modalities) at different time points. For longitudinal data, the temporal origin in the NIfTI header
identifies the time point that each input image belongs to. How all input images and polydata sets are
registered with one another is determined by an energy function. This energy function is formulated in
a simplified math expression using MATLAB-style indexing for the individual input files, i.e.,</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/remesh-surface.html"><span class="doc">remesh-surface</span></a></td>
<td>Remeshes a surface mesh such that the resulting mesh has an average
edge length within the specified limits. The input surface mesh is
triangulated when necessary before the local remeshing passes.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/resample-image.html"><span class="doc">resample-image</span></a></td>
<td>Resamples an image on a lattice with specified voxel size.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/smooth-image.html"><span class="doc">smooth-image</span></a></td>
<td>This program blurs an input image using a Gaussian filter with a standard
deviation equal to the specified sigma value. The dimensions in which the
filter recursively applied can be specified by the respective options below.
Note that more than one of these options can be specified and that each can
also be given more than once. The blurring of the respective dimensions
is then performed in the order of the given blurring options.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/smooth-surface.html"><span class="doc">smooth-surface</span></a></td>
<td>Smooths the node positions and/or scalar data of a surface mesh.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/split-labels.html"><span class="doc">split-labels</span></a></td>
<td>Measures the probability of the different labels in the N label maps <labelmap_1> .. <labelmap_N>
according to the weights (maps) <weight_1> .. <weight_N> (based on occurence).
It then outputs the probability of the specified R labels <label_1> .. <label_R> to <probmap_1> .. <probmap_R></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/subdivide-brain-image.html"><span class="doc">subdivide-brain-image</span></a></td>
<td>This program reads a structural brain segmentation and derives from it
a segmentation of the brain volume into the following output labels.
This output segmentation can then be used to reconstruct topologically
correct (i.e., closed genus-0) surfaces of the cGM/WM interface for the
left and right hemisphere, where subcortical and deep brain structures
are enclosed by these so-called white surfaces. Additionally, the
brainstem+cerebellum segment can be respresented by another closed
surface mesh. The union of these reconstructured surfaces encloses
the entire brain volume, yet excluding cortical grey matter.
By deforming the joint brain surface towards the cGM/CSF interface,
the pial surface which encloses the entire brain volume including
subcortical structures can be obtained. The right/left hemisphere
assignment of cortical grey matter follows from the point correspondences
between white and pial surfaces, respectively, the RH/LH label may
be assigned to white surface mesh nodes upon merging the right/left
white surface meshes. See merge-surfaces -source-array option.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="commands/transform-image.html"><span class="doc">transform-image</span></a></td>
<td>Applies one or more transformations to an input image. Each voxel center
of the target image is mapped by the composition of the transformations to
the space of the source image. The output intensity for the target voxel is
the source image intensity interpolated at the mapped point and cast to
the output data type. When the input transformation is the identity map,
this command effectively resamples the input image on the finite discrete
grid of the <a class="reference internal" href="commands/transform-image.html#cmdoption-transform-image-target"><code class="xref std std-option docutils literal"><span class="pre">transform-image</span> <span class="pre">-target</span></code></a> image.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="commands/transform-points.html"><span class="doc">transform-points</span></a></td>
<td>Applies one or more transformations to a set of points. Input point
x, y, and z coordinates are either read from STDIN (space separated) or from a
point set file. The corresponding transformed coordinates are then written
either to STDOUT or an output point set file, respectively. If multiple
transformations are specified, these are applied in the order as they appear
on the command line.</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="options">
<h2>Options<a class="headerlink" href="#options" title="Permalink to this headline">¶</a></h2>
<p>The following options are common to all <code class="docutils literal"><span class="pre">mirtk</span></code> commands.
For a complete list of options for each command, see the help page of the respective
command <a class="reference internal" href="#commandssummary"><span class="std std-ref">linked above</span></a> or the command help (<code class="docutils literal"><span class="pre">mirtk</span> <span class="pre">help</span> <span class="pre"><command></span></code>).</p>
<div class="section" id="standard-options">
<h3>Standard options<a class="headerlink" href="#standard-options" title="Permalink to this headline">¶</a></h3>
<dl class="option">
<dt id="cmdoption-v">
<span id="cmdoption-verbose"></span><code class="descname">-v</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">-verbose</code><code class="descclassname"> [n]</code><a class="headerlink" href="#cmdoption-v" title="Permalink to this definition">¶</a></dt>
<dd><p>Increase/Set verbosity of output messages. (default: 0)</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-debug">
<code class="descname">-debug</code><code class="descclassname"> [level]</code><a class="headerlink" href="#cmdoption-debug" title="Permalink to this definition">¶</a></dt>
<dd><p>Increase/Set debug level for output of intermediate results. (default: 0)</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-version">
<code class="descname">-version</code><code class="descclassname"> [major.minor]</code><a class="headerlink" href="#cmdoption-version" title="Permalink to this definition">¶</a></dt>
<dd><p>Print version and exit or set version to emulate.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-revision">
<code class="descname">-revision</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-revision" title="Permalink to this definition">¶</a></dt>
<dd><p>Print revision (or version) number only and exit.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-h">
<span id="cmdoption-help"></span><code class="descname">-h</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">-help</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-h" title="Permalink to this definition">¶</a></dt>
<dd><p>Print help and exit.</p>
</dd></dl>
</div>
<div class="section" id="terminal-options">
<h3>Terminal options<a class="headerlink" href="#terminal-options" title="Permalink to this headline">¶</a></h3>
<dl class="option">
<dt id="cmdoption-color">
<span id="cmdoption-nocolor"></span><code class="descname">-color</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">-nocolor</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-color" title="Permalink to this definition">¶</a></dt>
<dd><p>Enable/disable colored output. (default: off)</p>
</dd></dl>
</div>
<div class="section" id="parallelization-options">
<h3>Parallelization options<a class="headerlink" href="#parallelization-options" title="Permalink to this headline">¶</a></h3>
<dl class="option">
<dt id="cmdoption-threads">
<code class="descname">-threads</code><code class="descclassname"> <n></code><a class="headerlink" href="#cmdoption-threads" title="Permalink to this definition">¶</a></dt>
<dd><p>Use maximal <n> threads for parallel execution. (default: automatic)</p>
</dd></dl>
</div>
</div>
</div>
</div>
</div>
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