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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>Mia Program Reference</title><link rel="stylesheet" type="text/css" href="progref.css"><meta name="generator" content="DocBook XSL Stylesheets V1.79.1"><meta name="description" content="This reference document contains desctriptions for the command line tools and plug-ins provided by the MIA toolkit. To learn more about MIA please visit the web site http://mia.sourceforge.net"><link rel="home" href="index.html" title="Mia Program Reference"><link rel="next" href="ch01.html" title="Chapter 1. Introduction"></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 Program Reference</th></tr><tr><td width="20%" align="left"> </td><th width="60%" align="center"> </th><td width="20%" align="right"> <a accesskey="n" href="ch01.html">Next</a></td></tr></table><hr></div><div class="book"><div class="titlepage"><div><div><h1 class="title"><a name="idp1"></a>Mia Program Reference</h1></div><div><div class="author"><h3 class="author"><span class="firstname">Gert</span> <span class="surname">Wollny</span></h3></div></div><div><div class="abstract"><p class="title"><b>Abstract</b></p>
<p>
This reference document contains desctriptions for the command line tools and plug-ins
provided by the MIA toolkit.
To learn more about MIA please visit the web site <a class="ulink" href="http://mia.sourceforge.net" target="_top">http://mia.sourceforge.net</a>
</p>
</div></div></div><hr></div><div class="toc"><p><b>Table of Contents</b></p><dl class="toc"><dt><span class="chapter"><a href="ch01.html">1. Introduction</a></span></dt><dt><span class="chapter"><a href="ch02.html">2. Program Reference</a></span></dt><dd><dl><dt><span class="section"><a href="SecImageconversion.html">Image conversion</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2dimageselect.html">mia-2dimageselect</a></span></dt><dt><span class="section"><a href="Secmia2dmultiimageto3d.html">mia-2dmultiimageto3d</a></span></dt><dt><span class="section"><a href="Secmia2dto3dimage.html">mia-2dto3dimage</a></span></dt><dt><span class="section"><a href="Secmia2dto3dimageb.html">mia-2dto3dimageb</a></span></dt><dt><span class="section"><a href="Secmia3dgetslice.html">mia-3dgetslice</a></span></dt><dt><span class="section"><a href="Secmia3dimageselect.html">mia-3dimageselect</a></span></dt><dt><span class="section"><a href="Secmiaraw2image.html">mia-raw2image</a></span></dt><dt><span class="section"><a href="Secmiaraw2volume.html">mia-raw2volume</a></span></dt></dl></dd><dt><span class="section"><a href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Analysis, filtering, combining, and segmentation of 2D images</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2davgmasked.html">mia-2davgmasked</a></span></dt><dt><span class="section"><a href="Secmia2dbinarycombine.html">mia-2dbinarycombine</a></span></dt><dt><span class="section"><a href="Secmia2ddistance.html">mia-2ddistance</a></span></dt><dt><span class="section"><a href="Secmia2dfuzzysegment.html">mia-2dfuzzysegment</a></span></dt><dt><span class="section"><a href="Secmia2dgrayimagecombinetorgb.html">mia-2dgrayimage-combine-to-rgb</a></span></dt><dt><span class="section"><a href="Secmia2dimagecombinedice.html">mia-2dimagecombine-dice</a></span></dt><dt><span class="section"><a href="Secmia2dimagecombiner.html">mia-2dimagecombiner</a></span></dt><dt><span class="section"><a href="Secmia2dimagecreator.html">mia-2dimagecreator</a></span></dt><dt><span class="section"><a href="Secmia2dimagefilter.html">mia-2dimagefilter</a></span></dt><dt><span class="section"><a href="Secmia2dimagefilterstack.html">mia-2dimagefilterstack</a></span></dt><dt><span class="section"><a href="Secmia2dimagefullstats.html">mia-2dimagefullstats</a></span></dt><dt><span class="section"><a href="Secmia2dimageseriesmaximumintensityprojection.html">mia-2dimageseries-maximum-intensity-projection</a></span></dt><dt><span class="section"><a href="Secmia2dimagestats.html">mia-2dimagestats</a></span></dt><dt><span class="section"><a href="Secmia2dlerp.html">mia-2dlerp</a></span></dt><dt><span class="section"><a href="Secmia2dmultiimagevar.html">mia-2dmultiimagevar</a></span></dt><dt><span class="section"><a href="Secmia2dsegmentahmed.html">mia-2dsegment-ahmed</a></span></dt><dt><span class="section"><a href="Secmia2dsegmentfuzzyw.html">mia-2dsegment-fuzzyw</a></span></dt><dt><span class="section"><a href="Secmia2dsegmentlocalcmeans.html">mia-2dsegment-local-cmeans</a></span></dt><dt><span class="section"><a href="Secmia2dsegmentlocalkmeans.html">mia-2dsegment-local-kmeans</a></span></dt><dt><span class="section"><a href="Secmia2dsegmentperpixelkmeans.html">mia-2dsegment-per-pixel-kmeans</a></span></dt></dl></dd><dt><span class="section"><a href="SecRegistrationComparisonandTransformationof2Dimages.html">Registration, Comparison, and Transformation of 2D images</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2dcost.html">mia-2dcost</a></span></dt><dt><span class="section"><a href="Secmia2ddeform.html">mia-2ddeform</a></span></dt><dt><span class="section"><a href="Secmia2dfluid.html">mia-2dfluid</a></span></dt><dt><span class="section"><a href="Secmia2dforce.html">mia-2dforce</a></span></dt><dt><span class="section"><a href="Secmia2dimageregistration.html">mia-2dimageregistration</a></span></dt><dt><span class="section"><a href="Secmia2dmultiforce.html">mia-2dmulti-force</a></span></dt><dt><span class="section"><a href="Secmia2dmultiimageregistration.html">mia-2dmultiimageregistration</a></span></dt><dt><span class="section"><a href="Secmia2dtransform.html">mia-2dtransform</a></span></dt><dt><span class="section"><a href="Secmia2dtransformationtostrain.html">mia-2dtransformation-to-strain</a></span></dt></dl></dd><dt><span class="section"><a href="SecRegistrationofseriesof2Dimages.html">Registration of series of 2D images</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2dgroundtruthreg.html">mia-2dgroundtruthreg</a></span></dt><dt><span class="section"><a href="Secmia2dmany2onenonrigid.html">mia-2dmany2one-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia2dmyoicafull.html">mia-2dmyoica-full</a></span></dt><dt><span class="section"><a href="Secmia2dmyoicanonrigid.html">mia-2dmyoica-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia2dmyoicanonrigidparallel.html">mia-2dmyoica-nonrigid-parallel</a></span></dt><dt><span class="section"><a href="Secmia2dmyoicanonrigid2.html">mia-2dmyoica-nonrigid2</a></span></dt><dt><span class="section"><a href="Secmia2dmyoicapgt.html">mia-2dmyoicapgt</a></span></dt><dt><span class="section"><a href="Secmia2dmyomilles.html">mia-2dmyomilles</a></span></dt><dt><span class="section"><a href="Secmia2dmyoperiodicnonrigid.html">mia-2dmyoperiodic-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia2dmyopgtnonrigid.html">mia-2dmyopgt-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia2dmyoserialnonrigid.html">mia-2dmyoserial-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia2dmyosetall2onenonrigid.html">mia-2dmyoset-all2one-nonrigid</a></span></dt></dl></dd><dt><span class="section"><a href="SecToolsfortheAnalysisof2Dimageseries.html">Tools for the Analysis of 2D image series</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2devaltransformquantity.html">mia-2deval-transformquantity</a></span></dt><dt><span class="section"><a href="Secmia2dtrackpixelmovement.html">mia-2dtrackpixelmovement</a></span></dt></dl></dd><dt><span class="section"><a href="SecToolsforMyocardialPerfusionAnalysis.html">Tools for Myocardial Perfusion Analysis</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2dmyocardica.html">mia-2dmyocard-ica</a></span></dt><dt><span class="section"><a href="Secmia2dmyocardicaseries.html">mia-2dmyocard-icaseries</a></span></dt><dt><span class="section"><a href="Secmia2dmyoseriescompdice.html">mia-2dmyoseries-compdice</a></span></dt><dt><span class="section"><a href="Secmia2dmyoseriesdice.html">mia-2dmyoseries-dice</a></span></dt><dt><span class="section"><a href="Secmia2dsegcompare.html">mia-2dsegcompare</a></span></dt><dt><span class="section"><a href="Secmia2dseghausdorff.html">mia-2dseghausdorff</a></span></dt><dt><span class="section"><a href="Secmia2dsegmentcropbox.html">mia-2dsegmentcropbox</a></span></dt><dt><span class="section"><a href="Secmia2dsegseriesstats.html">mia-2dsegseriesstats</a></span></dt><dt><span class="section"><a href="Secmia2dsegshift.html">mia-2dsegshift</a></span></dt><dt><span class="section"><a href="Secmia2dsegshiftperslice.html">mia-2dsegshiftperslice</a></span></dt><dt><span class="section"><a href="Secmia2dseriesmincorr.html">mia-2dseries-mincorr</a></span></dt><dt><span class="section"><a href="Secmia2dseriessectionmask.html">mia-2dseries-sectionmask</a></span></dt><dt><span class="section"><a href="Secmia2dseriessegdistance.html">mia-2dseries-segdistance</a></span></dt><dt><span class="section"><a href="Secmia2dseries2dordermedian.html">mia-2dseries2dordermedian</a></span></dt><dt><span class="section"><a href="Secmia2dseries2sets.html">mia-2dseries2sets</a></span></dt><dt><span class="section"><a href="Secmia2dseriescorr.html">mia-2dseriescorr</a></span></dt><dt><span class="section"><a href="Secmia2dseriesgradMAD.html">mia-2dseriesgradMAD</a></span></dt><dt><span class="section"><a href="Secmia2dseriesgradvariation.html">mia-2dseriesgradvariation</a></span></dt><dt><span class="section"><a href="Secmia2dserieshausdorff.html">mia-2dserieshausdorff</a></span></dt><dt><span class="section"><a href="Secmia2dseriessmoothgradMAD.html">mia-2dseriessmoothgradMAD</a></span></dt><dt><span class="section"><a href="Secmia2dseriestovolume.html">mia-2dseriestovolume</a></span></dt></dl></dd><dt><span class="section"><a href="SecProcessingofseriesof2Dimagesina3Dfashionoutofcore.html">Processing of series of 2D images in a 3D fashion (out-of-core)</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2dimagestackcmeans.html">mia-2dimagestack-cmeans</a></span></dt><dt><span class="section"><a href="Secmia2dstackcmeanspresegment.html">mia-2dstack-cmeans-presegment</a></span></dt><dt><span class="section"><a href="Secmia2dstackfilter.html">mia-2dstackfilter</a></span></dt><dt><span class="section"><a href="Secmia3ddistance.html">mia-3ddistance</a></span></dt><dt><span class="section"><a href="Secmiamultihist.html">mia-multihist</a></span></dt></dl></dd><dt><span class="section"><a href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Analysis, filtering, combining, and segmentation of 3D images</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia3dbinarycombine.html">mia-3dbinarycombine</a></span></dt><dt><span class="section"><a href="Secmia3dbrainextractT1.html">mia-3dbrainextractT1</a></span></dt><dt><span class="section"><a href="Secmia3dcombineimageseries.html">mia-3dcombine-imageseries</a></span></dt><dt><span class="section"><a href="Secmia3dcombinemrsegmentations.html">mia-3dcombine-mr-segmentations</a></span></dt><dt><span class="section"><a href="Secmia3dcrispsegment.html">mia-3dcrispsegment</a></span></dt><dt><span class="section"><a href="Secmia3ddistancestats.html">mia-3ddistance-stats</a></span></dt><dt><span class="section"><a href="Secmia3dfuzzysegment.html">mia-3dfuzzysegment</a></span></dt><dt><span class="section"><a href="Secmia3dgetsize.html">mia-3dgetsize</a></span></dt><dt><span class="section"><a href="Secmia3dimagecombine.html">mia-3dimagecombine</a></span></dt><dt><span class="section"><a href="Secmia3dimagecreator.html">mia-3dimagecreator</a></span></dt><dt><span class="section"><a href="Secmia3dimagefilter.html">mia-3dimagefilter</a></span></dt><dt><span class="section"><a href="Secmia3dimagefilterstack.html">mia-3dimagefilterstack</a></span></dt><dt><span class="section"><a href="Secmia3dimagestatisticsinmask.html">mia-3dimagestatistics-in-mask</a></span></dt><dt><span class="section"><a href="Secmia3dimagestats.html">mia-3dimagestats</a></span></dt><dt><span class="section"><a href="Secmia3disosurfacefromstack.html">mia-3disosurface-from-stack</a></span></dt><dt><span class="section"><a href="Secmia3dlerp.html">mia-3dlerp</a></span></dt><dt><span class="section"><a href="Secmia3dmaskseeded.html">mia-3dmaskseeded</a></span></dt><dt><span class="section"><a href="Secmia3dproposeboundingbox.html">mia-3dpropose-boundingbox</a></span></dt><dt><span class="section"><a href="Secmia3dsegmentahmed.html">mia-3dsegment-ahmed</a></span></dt></dl></dd><dt><span class="section"><a href="SecRegistrationComparisonandTransformationof3Dimages.html">Registration, Comparison, and Transformation of 3D images</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia3dcost.html">mia-3dcost</a></span></dt><dt><span class="section"><a href="Secmia3dcosttranslatedgrad.html">mia-3dcost-translatedgrad</a></span></dt><dt><span class="section"><a href="Secmia3ddeform.html">mia-3ddeform</a></span></dt><dt><span class="section"><a href="Secmia3dfluid.html">mia-3dfluid</a></span></dt><dt><span class="section"><a href="Secmia3dforce.html">mia-3dforce</a></span></dt><dt><span class="section"><a href="Secmia3dlandmarksdistances.html">mia-3dlandmarks-distances</a></span></dt><dt><span class="section"><a href="Secmia3dlandmarkstransform.html">mia-3dlandmarks-transform</a></span></dt><dt><span class="section"><a href="Secmia3dnonrigidreg.html">mia-3dnonrigidreg</a></span></dt><dt><span class="section"><a href="Secmia3dnonrigidregalt.html">mia-3dnonrigidreg-alt</a></span></dt><dt><span class="section"><a href="Secmia3drigidreg.html">mia-3drigidreg</a></span></dt><dt><span class="section"><a href="Secmia3dtransform.html">mia-3dtransform</a></span></dt><dt><span class="section"><a href="Secmia3dtransform2vf.html">mia-3dtransform2vf</a></span></dt><dt><span class="section"><a href="Secmia3dvf2transform.html">mia-3dvf2transform</a></span></dt><dt><span class="section"><a href="Secmia3dvfcompare.html">mia-3dvfcompare</a></span></dt></dl></dd><dt><span class="section"><a href="SecRegistrationofseriesof3Dimages.html">Registration of series of 3D images</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia3dmany2onenonrigid.html">mia-3dmany2one-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia3dmotioncompicanonrigid.html">mia-3dmotioncompica-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia3dprealignnonrigid.html">mia-3dprealign-nonrigid</a></span></dt><dt><span class="section"><a href="Secmia3dserialnonrigid.html">mia-3dserial-nonrigid</a></span></dt></dl></dd><dt><span class="section"><a href="SecToolsfortheAnalysisof3Dimageseries.html">Tools for the Analysis of 3D image series</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia3devaltransformquantity.html">mia-3deval-transformquantity</a></span></dt><dt><span class="section"><a href="Secmia3dseriestrackintensity.html">mia-3dseries-track-intensity</a></span></dt><dt><span class="section"><a href="Secmia3dtrackpixelmovement.html">mia-3dtrackpixelmovement</a></span></dt></dl></dd><dt><span class="section"><a href="SecMiscellaneousprograms.html">Miscellaneous programs</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia3dfield2norm.html">mia-3dfield2norm</a></span></dt><dt><span class="section"><a href="Secmia3dimageaddattributes.html">mia-3dimageaddattributes</a></span></dt><dt><span class="section"><a href="Secmia3dvectorfieldcreate.html">mia-3dvectorfieldcreate</a></span></dt><dt><span class="section"><a href="Secmiacmeans.html">mia-cmeans</a></span></dt><dt><span class="section"><a href="Secmiafilenumberpattern.html">mia-filenumberpattern</a></span></dt><dt><span class="section"><a href="Secmialabelsort.html">mia-labelsort</a></span></dt><dt><span class="section"><a href="Secmiamyowavelettest.html">mia-myowavelettest</a></span></dt><dt><span class="section"><a href="Secmiawavelettrans.html">mia-wavelettrans</a></span></dt></dl></dd><dt><span class="section"><a href="SecCreationanalysisandfilteringoftriangular3Dmeshes.html">Creation, analysis, and filtering of triangular 3D meshes</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia3disosurfacefromvolume.html">mia-3disosurface-from-volume</a></span></dt><dt><span class="section"><a href="Secmiameshdeformablemodel.html">mia-mesh-deformable-model</a></span></dt><dt><span class="section"><a href="Secmiameshtomaskimage.html">mia-mesh-to-maskimage</a></span></dt><dt><span class="section"><a href="Secmiameshdistancetostackmask.html">mia-meshdistance-to-stackmask</a></span></dt><dt><span class="section"><a href="Secmiameshfilter.html">mia-meshfilter</a></span></dt></dl></dd><dt><span class="section"><a href="SecHelp.html">Help</a></span></dt><dd><dl><dt><span class="section"><a href="Secmiapluginhelp.html">mia-plugin-help</a></span></dt></dl></dd><dt><span class="section"><a href="SecWorkinprogress.html">Work in progress</a></span></dt><dd><dl><dt><span class="section"><a href="Secmia2dmyocardsegment.html">mia-2dmyocard-segment</a></span></dt></dl></dd></dl></dd><dt><span class="chapter"><a href="plugins.html">3. Plugin Reference</a></span></dt><dd><dl><dt><span class="section"><a href="SecPlugintype1dcmeans.html">Plugin type: 1d/cmeans</a></span></dt><dt><span class="section"><a href="SecPlugintype1dspacialkernel.html">Plugin type: 1d/spacialkernel</a></span></dt><dt><span class="section"><a href="SecPlugintype1dsplinebc.html">Plugin type: 1d/splinebc</a></span></dt><dt><span class="section"><a href="SecPlugintype1dsplinekernel.html">Plugin type: 1d/splinekernel</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagecombiner.html">Plugin type: 2dimage/combiner</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagecost.html">Plugin type: 2dimage/cost</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagecreator.html">Plugin type: 2dimage/creator</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagefilter.html">Plugin type: 2dimage/filter</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagefullcost.html">Plugin type: 2dimage/fullcost</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimageio.html">Plugin type: 2dimage/io</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagemaskedcost.html">Plugin type: 2dimage/maskedcost</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimageshape.html">Plugin type: 2dimage/shape</a></span></dt><dt><span class="section"><a href="SecPlugintype2dimagetransform.html">Plugin type: 2dimage/transform</a></span></dt><dt><span class="section"><a href="SecPlugintype2dstackfilter.html">Plugin type: 2dstack/filter</a></span></dt><dt><span class="section"><a href="SecPlugintype2dtransformio.html">Plugin type: 2dtransform/io</a></span></dt><dt><span class="section"><a href="SecPlugintype2dtransformsplinepenalty.html">Plugin type: 2dtransform/splinepenalty</a></span></dt><dt><span class="section"><a href="SecPlugintype2dvfio.html">Plugin type: 2dvf/io</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagecombiner.html">Plugin type: 3dimage/combiner</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagecost.html">Plugin type: 3dimage/cost</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagecreator.html">Plugin type: 3dimage/creator</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagefilter.html">Plugin type: 3dimage/filter</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagefullcost.html">Plugin type: 3dimage/fullcost</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimageio.html">Plugin type: 3dimage/io</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagemaskedcost.html">Plugin type: 3dimage/maskedcost</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimageshape.html">Plugin type: 3dimage/shape</a></span></dt><dt><span class="section"><a href="SecPlugintype3dimagetransform.html">Plugin type: 3dimage/transform</a></span></dt><dt><span class="section"><a href="SecPlugintype3dlandmarklistio.html">Plugin type: 3dlandmarklist/io</a></span></dt><dt><span class="section"><a href="SecPlugintype3dtransformio.html">Plugin type: 3dtransform/io</a></span></dt><dt><span class="section"><a href="SecPlugintype3dtransformsplinepenalty.html">Plugin type: 3dtransform/splinepenalty</a></span></dt><dt><span class="section"><a href="SecPlugintype3dvfio.html">Plugin type: 3dvf/io</a></span></dt><dt><span class="section"><a href="SecPlugintypegeneratornoise.html">Plugin type: generator/noise</a></span></dt><dt><span class="section"><a href="SecPlugintypemeshfilter.html">Plugin type: mesh/filter</a></span></dt><dt><span class="section"><a href="SecPlugintypemeshio.html">Plugin type: mesh/io</a></span></dt><dt><span class="section"><a href="SecPlugintypeminimizersinglecost.html">Plugin type: minimizer/singlecost</a></span></dt></dl></dd></dl></div>
</div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"> </td><td width="20%" align="center"> </td><td width="40%" align="right"> <a accesskey="n" href="ch01.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top"> </td><td width="20%" align="center"> </td><td width="40%" align="right" valign="top"> Chapter 1. Introduction</td></tr></table></div></body></html>
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