<div dir="ltr">Hi Pascal,<br><br>Welcome to the list and good first post!<br><br>The OrientImageFilter class is deprecated and not supported.<br><br>For more information, see [1] [2]<br><br>Thanks,<br>Matt<br><br>[1] <a href="http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates">http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates</a><br>
[2] <a href="http://www.slicer.org/slicerWiki/index.php/Coordinate_systems">http://www.slicer.org/slicerWiki/index.php/Coordinate_systems</a><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Nov 28, 2013 at 10:32 AM,  <span dir="ltr"><<a href="mailto:p.wettmann@hispeed.ch" target="_blank">p.wettmann@hispeed.ch</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">hi,<br>
<br>
I intend to read an arbitrary MRI file (e.g. RAI, ASL, ...) and convert it to RAI for further use. If i enter RAI, use orientImageFilter, output is correct RAI. However, if i enter ASL, output is not RAI. L/R axis is inverse. If I use LAI or a axis flip afterwards, the image seems to be correct, despite the fact that it is shifted.<br>

<br>
Here a code snipets:<br>
<br>
         typedef short PixelType;<br>
         const unsigned int VolumeDimension = 3;<br>
         typedef itk::Image< PixelType, VolumeDimension > ImageType;<br>
         typedef itk::ImageSeriesReader< ImageType >    ReaderType;<br>
<br>
         [...]<br>
<br>
         ReaderType::Pointer reader = ReaderType::New();<br>
<br>
         itk::OrientImageFilter<ImageType,ImageType>::Pointer orienter =<br>
         itk::OrientImageFilter<ImageType,ImageType>::New();<br>
<br>
         FlipImageFilterType::Pointer flipFilter<br>
            = FlipImageFilterType::New ();<br>
<br>
         [...]<br>
<br>
         reader->SetFileNames(fileNamesNew);<br>
         reader->Update();<br>
<br>
         rval = reader->GetOutput();<br>
<br>
         orienter->UseImageDirectionOn();<br>
         orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);<br>
         //orienter->SetDesiredCoordinateOrientationToAxial();<br>
         orienter->SetInput(rval);<br>
         orienter->Update();<br>
<br>
         rval = orienter->GetOutput();<br>
<br>
//         itk::FixedArray<bool, 3> flipAxes;<br>
//         flipAxes[0] = true;<br>
//         flipAxes[1] = false;<br>
//         flipAxes[2] = false;<br>
<br>
//         flipFilter->SetInput(rval);<br>
//         flipFilter->SetFlipAxes(flipAxes);<br>
<br>
<br>
Am I missing something? This is my first e-mail to a mailing list, so please let me know any improvements of posting or style. :)<br>
<br>
Thanks for any help!<br>
<br>
Pascal<br>
<br>
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</blockquote></div><br></div>