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1 2 3 4 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dmyoicapgt</title><link rel="stylesheet" type="text/css" href="progref.css"><meta name="generator" content="DocBook XSL Stylesheets V1.79.1"><link rel="home" href="index.html" title="Mia Program Reference"><link rel="up" href="SecRegistrationofseriesof2Dimages.html" title="Registration of series of 2D images"><link rel="prev" href="Secmia2dmyoicanonrigid2.html" title="mia-2dmyoica-nonrigid2"><link rel="next" href="Secmia2dmyomilles.html" title="mia-2dmyomilles"></head><body bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">mia-2dmyoicapgt</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dmyoicanonrigid2.html">Prev</a> </td><th width="60%" align="center">Registration of series of 2D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia2dmyomilles.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dmyoicapgt"></a>mia-2dmyoicapgt</h3></div></div></div><h4><a name="idp5027"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dmyoicapgt</code> {-i <em class="replaceable"><code>string</code></em>} {-o <em class="replaceable"><code>string</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp5036"></a>Description:</h4><p>This program implements a two passs motion compensation algorithm. First a linear registration is run based on a variation of Gupta et~al. "Fully automatic registration and segmentation of first-pass myocardial perfusion MR image sequences", Academic Radiology 17, 1375-1385 as described in in Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012, DOI:10.1016/j.media.2012.02.004, followed by a non-linear registration based Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009. Note that for this nonlinear motion correction a preceding linear registration step is usually required. This version of the program may run all registrations in parallel.</p><h4><a name="idp5038"></a>Options:</h4><h4><a name="idp5039"></a>
Pseudo Ground Thruth estimation</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-A, --alpha=0.1; double</span></dt><dd><p>spacial neighborhood penalty weightspacial neighborhood penalty weight</p></dd><dt><span class="term">-B, --beta=4; double</span></dt><dd><p>temporal second derivative penalty weighttemporal second derivative penalty weight</p></dd><dt><span class="term">-T, --rho-thresh=0.85; double</span></dt><dd><p>correlation threshold for neighborhood analysiscorrelation threshold for neighborhood analysis</p></dd></dl></div><h4><a name="idp5053"></a>File-IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-file=(input, required); string</span></dt><dd><p>input perfusion data set</p></dd><dt><span class="term">-o, --out-file=(output, required); string</span></dt><dd><p>output perfusion data set</p></dd><dt><span class="term">-r, --registered=STRING</span></dt><dd><p>File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.</p></dd><dt><span class="term">--save-cropped=(output); string</span></dt><dd><p>save cropped set to this file, the image files will use the stem of the name as file name base</p></dd><dt><span class="term">--save-feature=(output); string</span></dt><dd><p>save segmentation feature images and initial ICA mixing matrix</p></dd><dt><span class="term">--save-refs=(output); string</span></dt><dd><p>for each registration pass save the reference images to files with the given name base</p></dd><dt><span class="term">--save-regs=(output); string</span></dt><dd><p>for each registration pass save intermediate registered images</p></dd></dl></div><h4><a name="idp5083"></a>Help & Info</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-V, --verbose=warning; dict</span></dt><dd><p>verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:</p><div class="informaltable"><table class="informaltable" border="0"><colgroup><col class="c1"><col class="c2"></colgroup><tbody><tr><td align="left" valign="top">info:</td><td align="left" valign="top">Low level messages</td></tr><tr><td align="left" valign="top">trace:</td><td align="left" valign="top">Function call trace</td></tr><tr><td align="left" valign="top">fail:</td><td align="left" valign="top">Report test failures</td></tr><tr><td align="left" valign="top">warning:</td><td align="left" valign="top">Warnings</td></tr><tr><td align="left" valign="top">error:</td><td align="left" valign="top">Report errors</td></tr><tr><td align="left" valign="top">debug:</td><td align="left" valign="top">Debug output</td></tr><tr><td align="left" valign="top">message:</td><td align="left" valign="top">Normal messages</td></tr><tr><td align="left" valign="top">fatal:</td><td align="left" valign="top">Report only fatal errors</td></tr></tbody></table></div></dd><dt><span class="term">--copyright=(); bool</span></dt><dd><p>print copyright information</p></dd><dt><span class="term">-h, --help=(); bool</span></dt><dd><p>print this help</p></dd><dt><span class="term">-?, --usage=(); bool</span></dt><dd><p>print a short help</p></dd><dt><span class="term">--version=(); bool</span></dt><dd><p>print the version number and exit</p></dd></dl></div><h4><a name="idp5134"></a>ICA</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-C, --components=0; ulong</span></dt><dd><p>ICA components 0 = automatic estimationICA components 0 = automatic estimation</p></dd><dt><span class="term">--normalize</span></dt><dd><p>normalized ICs</p></dd><dt><span class="term">--no-meanstrip</span></dt><dd><p>don't strip the mean from the mixing curves</p></dd><dt><span class="term">-s, --segscale=0; float</span></dt><dd><p>segment and scale the crop box around the LV (0=no segmentation)segment and scale the crop box around the LV (0=no segmentation)</p></dd><dt><span class="term">-k, --skip=0; ulong</span></dt><dd><p>skip images at the beginning of the series e.g. because as they are of other modalitiesskip images at the beginning of the series e.g. because as they are of other modalities</p></dd><dt><span class="term">-m, --max-ica-iter=400; ulong</span></dt><dd><p>maximum number of iterations in ICAmaximum number of iterations in ICA</p></dd><dt><span class="term">-E, --segmethod=features; dict</span></dt><dd><p>Segmentation method</p><div class="informaltable"><table class="informaltable" border="0"><colgroup><col class="c1"><col class="c2"></colgroup><tbody><tr><td align="left" valign="top">delta-peak:</td><td align="left" valign="top">difference of the peak enhancement images</td></tr><tr><td align="left" valign="top">features:</td><td align="left" valign="top">feature images</td></tr><tr><td align="left" valign="top">delta-feature:</td><td align="left" valign="top">difference of the feature images</td></tr></tbody></table></div></dd><dt><span class="term">-b, --min-breathing-frequency=-1; float</span></dt><dd><p>minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.</p></dd></dl></div><h4><a name="idp5182"></a>Processing</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">--threads=-1; int</span></dt><dd><p>Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).</p></dd></dl></div><h4><a name="idp5188"></a>Registration</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory</span></dt><dd><p>Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see <a class="xref" href="SecPlugintypeminimizersinglecost.html" title="Plugin type: minimizer/singlecost">Plugin type: minimizer/singlecost</a></p></dd><dt><span class="term">--linear-transform=affine; factory</span></dt><dd><p>linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagetransform.html" title="Plugin type: 2dimage/transform">Plugin type: 2dimage/transform</a></p></dd><dt><span class="term">-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory</span></dt><dd><p>Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see <a class="xref" href="SecPlugintypeminimizersinglecost.html" title="Plugin type: minimizer/singlecost">Plugin type: minimizer/singlecost</a></p></dd><dt><span class="term">-a, --start-c-rate=16; double</span></dt><dd><p>start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.</p></dd><dt><span class="term">--c-rate-divider=2; double</span></dt><dd><p>Cofficient rate divider for each pass.Cofficient rate divider for each pass.</p></dd><dt><span class="term">-d, --start-divcurl=10000; double</span></dt><dd><p>Start divcurl weight, gets divided by --divcurl-divider with every pass.Start divcurl weight, gets divided by --divcurl-divider with every pass.</p></dd><dt><span class="term">--divcurl-divider=2; double</span></dt><dd><p>Divcurl weight scaling with each new pass.Divcurl weight scaling with each new pass.</p></dd><dt><span class="term">-R, --reference=-1; int</span></dt><dd><p>Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movementGlobal reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement</p></dd><dt><span class="term">-w, --imagecost=image:weight=1,cost=ssd; factory</span></dt><dd><p>image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see <a class="xref" href="SecPlugintype2dimagefullcost.html" title="Plugin type: 2dimage/fullcost">Plugin type: 2dimage/fullcost</a></p></dd><dt><span class="term">-l, --mg-levels=3; ulong</span></dt><dd><p>multi-resolution levelsmulti-resolution levels</p></dd><dt><span class="term">-p, --linear-passes=3; ulong</span></dt><dd><p>linear registration passes (0 to disable)linear registration passes (0 to disable)</p></dd><dt><span class="term">-P, --nonlinear-passes=3; ulong</span></dt><dd><p>non-linear registration passes (0 to disable)non-linear registration passes (0 to disable)</p></dd></dl></div><h4><a name="idp5242"></a>Example:</h4><p>Register the perfusion series given in 'segment.set' by first using automatic ICA estimation to run the linear registration and then the PGT registration. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.</p><pre class="screen">mia-2dmyoicapgt -i segment.set -o registered.set -k 2</pre><h4><a name="idp5245"></a>Author(s):</h4><p>Gert Wollny</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="Secmia2dmyoicanonrigid2.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecRegistrationofseriesof2Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia2dmyomilles.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dmyoica-nonrigid2 </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dmyomilles</td></tr></table></div></body></html>
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