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<div>Yves,</div>
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<div>It looks like the Transformation matrix is not orthogonal. The OrientImageFilter requires that the matrix defines three orthogonal vectors. I would recommend not using this filter and deal with the image in Physical space versus voxel space.</div>
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<div>Vince</div>
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<div>-- </div>
<div><font face="Calibri,Verdana,Helvetica,Arial"><span style="font-size:11pt">Associate Professor<br>
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<span style="font-weight:bold">From: </span>Yves Martelli <<a href="mailto:ymartelli@cistib.upf.edu">ymartelli@cistib.upf.edu</a>><br>
<span style="font-weight:bold">Date: </span>Thu, 24 Mar 2011 16:37:42 +0100<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>><br>
<span style="font-weight:bold">Subject: </span>[Insight-users] itk::PermuteAxesImageFilter: Order indices must not repeat<br>
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<p class="MsoNormal"><span lang="EN-US">Dear list,</span></p>
<p class="MsoNormal"><span lang="EN-US">I am trying to reorient an itk::Image using the itk::OrientImageFilter in ITK version 3.20 but I run into the ‘Order indices must not repeat’ error from the itk::PermuteAxesImageFilter used inside the orient filter.
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<p class="MsoNormal"><span lang="EN-US">Here is the mhd header of my data:</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">ObjectType = Image</span></p>
<p class="MsoNormal"><span lang="EN-US">NDims = 3</span></p>
<p class="MsoNormal"><span lang="EN-US">BinaryData = True</span></p>
<p class="MsoNormal"><span lang="EN-US">BinaryDataByteOrderMSB = False</span></p>
<p class="MsoNormal"><span lang="EN-US">CompressedData = False</span></p>
<p class="MsoNormal"><span lang="EN-US">TransformMatrix = 0.828301 0.488478 0.274421 -0.533463 0.537852 0.652789 0.171276 -0.687099 0.706088</span></p>
<p class="MsoNormal"><span lang="EN-US">Offset = -5.73852 -56.2626 -66.4521</span></p>
<p class="MsoNormal"><span lang="EN-US">CenterOfRotation = 0 0 0</span></p>
<p class="MsoNormal"><span lang="EN-US">AnatomicalOrientation = RPI</span></p>
<p class="MsoNormal"><span lang="EN-US">ElementSpacing = 0.964286 0.964286 0.964286</span></p>
<p class="MsoNormal"><span lang="EN-US">DimSize = 112 112 111</span></p>
<p class="MsoNormal"><span lang="EN-US">ElementType = MET_FLOAT</span></p>
<p class="MsoNormal"><span lang="EN-US">ElementDataFile = image.raw</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">And this is what I am trying to do:</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">orienter->UseImageDirectionOn();</span></p>
<p class="MsoNormal"><span lang="EN-US">orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);</span></p>
<p class="MsoNormal"><span lang="EN-US">orienter->SetInput( reader->GetOutput() );</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Is there a problem with its orientation that makes it incompatible with the permute filter? Are they any limitations in terms of orientations for the orient filter? Or is there an error in the image file?</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Best,</span></p>
<p class="MsoNormal"><span lang="EN-US">Yves</span></p>
<p class="MsoNormal"><span lang="EN-GB"> </span></p>
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