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<!DOCTYPE html>
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<h1>Reformat an image with a CMTK registration using the reformatx tool</h1>
<small class="dont-index">Source: <a href="https://github.com/natverse/nat/blob/HEAD/R/cmtk-reformat.R" class="external-link"><code>R/cmtk-reformat.R</code></a></small>
<div class="hidden name"><code>cmtk.reformatx.Rd</code></div>
</div>
<div class="ref-description">
<p>Reformat an image with a CMTK registration using the reformatx tool</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">cmtk.reformatx</span><span class="op">(</span>
<span class="va">floating</span>,
<span class="va">registrations</span>,
<span class="va">output</span>,
<span class="va">target</span>,
mask <span class="op">=</span> <span class="cn">FALSE</span>,
direction <span class="op">=</span> <span class="cn">NULL</span>,
interpolation <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"linear"</span>, <span class="st">"nn"</span>, <span class="st">"cubic"</span>, <span class="st">"pv"</span>, <span class="st">"sinc-cosine"</span>, <span class="st">"sinc-hamming"</span><span class="op">)</span>,
dryrun <span class="op">=</span> <span class="cn">FALSE</span>,
Verbose <span class="op">=</span> <span class="cn">TRUE</span>,
MakeLock <span class="op">=</span> <span class="cn">TRUE</span>,
OverWrite <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"no"</span>, <span class="st">"update"</span>, <span class="st">"yes"</span><span class="op">)</span>,
filesToIgnoreModTimes <span class="op">=</span> <span class="cn">NULL</span>,
<span class="va">...</span>
<span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>floating</dt>
<dd><p>The floating image to be reformatted</p></dd>
<dt>registrations</dt>
<dd><p>One or more CMTK format registrations on disk</p></dd>
<dt>output</dt>
<dd><p>The path to the output image (defaults to
<code>"<targetstem>_<floatingstem>.nrrd"</code>)</p></dd>
<dt>target</dt>
<dd><p>A character vector specifying an image file on disk, an
<code>im3d</code> object (or an object that can be coerced to im3d) or a 6-or
9-vector defining a grid in the form Nx,Ny,Nz,dX,dY,dZ,[Ox,Oy,Oz].</p></dd>
<dt>mask</dt>
<dd><p>Whether to treat target as a binary mask (only reformatting
positive voxels)</p></dd>
<dt>direction</dt>
<dd><p>Whether to transform image from sample space to reference
space (called <strong>forward</strong> by CMTK) or from reference to sample space
(called <strong>inverse</strong> by CMTK). Default (when <code>NULL</code> is forward).</p></dd>
<dt>interpolation</dt>
<dd><p>What interpolation scheme to use for output image
(defaults to linear - see details)</p></dd>
<dt>dryrun</dt>
<dd><p>Just print command</p></dd>
<dt>Verbose</dt>
<dd><p>Whether to show cmtk status messages and be verbose about file
update checks. Sets command line <code>--verbose</code> option.</p></dd>
<dt>MakeLock</dt>
<dd><p>Whether to use a lock file to allow simple parallelisation
(see <code>makelock</code>)</p></dd>
<dt>OverWrite</dt>
<dd><p>Whether to OverWrite an existing output file. One of
c("no","update","yes"). When OverWrite='update'
<code>RunCmdForNewerInput</code> is used to determine if the output is
older than any of the input files.</p></dd>
<dt>filesToIgnoreModTimes</dt>
<dd><p>Input files whose modification time should not
be checked when determining if new output is required.</p></dd>
<dt>...</dt>
<dd><p>additional arguments passed to CMTK <code>reformatx</code> after
processing by <code><a href="cmtk.call.html">cmtk.call</a></code>.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>the path to the output image (whether or not it was re-created afresh)
or <code>NA_character_</code> if no output was possible.</p>
</div>
<div id="details">
<h2>Details</h2>
<p>Note that if you are reformatting a mask then you will need to
change the interpolation to "nn", since interpolating between e.g. mask
levels 72 and 74 with 73 may have unintended consequences. Presently we
have no way of knowing whether an image should be treated as a mask, so the
<code>interpolation</code> must be handled manually.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><code><a href="cmtk.bindir.html">cmtk.bindir</a>, <a href="cmtk.call.html">cmtk.call</a>, makelock,
RunCmdForNewerInput</code></p></div>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span>
<span class="r-in"><span class="fu">cmtk.reformatx</span><span class="op">(</span><span class="st">'myimage.nrrd'</span>, target<span class="op">=</span><span class="st">'template.nrrd'</span>,</span>
<span class="r-in"> registrations<span class="op">=</span><span class="st">'template_myimage.list'</span><span class="op">)</span></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># get full listing of command line options </span></span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.html" class="external-link">system</a></span><span class="op">(</span><span class="fu"><a href="cmtk.call.html">cmtk.call</a></span><span class="op">(</span><span class="st">'reformatx'</span>, help<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
<span class="r-in"><span class="op">}</span></span>
</code></pre></div>
</div>
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