Hi guys,<br><br>I am trying to convert the AnatomicalOrientation of a 3D MRI from RPI to RSA using OrientImageFilter. <br><br><br>However, the entry &quot;AnatomicalOrientation&quot; in the header of the output *mha file is always RPI. itkSNAP was not able to interpret the anatomical orientation as RSA either. 

so my question is: 1. is it a bug in OrientImageFilter? 2. How to verify the AnatomicalOrientation of a *.nii or *.mha file? should I look at the header of meta data? or load them into Slicer3 or SNAP?

<br><br>The data can be accessed at <a href="http://www.duke.edu/~kurtzhao/RPI.zip">http://www.duke.edu/~kurtzhao/RPI.zip</a><br>The code is enclosed:<br><br>Thanks a lot!<br>-Kurt<br><br><br>#include &lt;iostream&gt;<br>

<br><br>#include &lt;metaCommand.h&gt;<br>#include &lt;itkImageFileWriter.h&gt;<br>#include &lt;itkImageFileReader.h&gt;<br>#include &lt;itkAnalyzeImageIO.h&gt;<br>#include &lt;itkNiftiImageIO.h&gt;<br>#include &lt;itkOrientImageFilter.h

&gt;<br>#include &lt;itkSpatialOrientation.h&gt;<br><br><br><br>int main(int argc, char **argv)<br>&nbsp; {<br><br>&nbsp; /** <br>&nbsp;&nbsp; * Typedefs and test reading to determine correct image types.<br>&nbsp;&nbsp; * *******************************************************************

<br>&nbsp;&nbsp; */<br><br>&nbsp; /** Initial image type. */<br>&nbsp; const unsigned int&nbsp;&nbsp;&nbsp; Dimension&nbsp; =&nbsp; 3;<br>&nbsp; //typedef float PixelType;<br>&nbsp; typedef short PixelType;<br><br>&nbsp; /** Some typedef&#39;s. */<br>&nbsp; typedef itk::Image&lt; PixelType, Dimension &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ImageType;

<br>&nbsp; typedef itk::ImageFileReader&lt; ImageType &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ReaderType;<br>&nbsp; typedef itk::ImageIOBase&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ImageIOBaseType;<br><br>&nbsp; ReaderType::Pointer reader = ReaderType::New();<br><br>&nbsp; itk::AnalyzeImageIO::Pointer io = itk::AnalyzeImageIO::New();

<br><br>&nbsp; //reader -&gt; SetImageIO ( io ) ;<br>&nbsp; /** Setup the Reader. */<br>&nbsp; std::string inputFileName; <br>&nbsp; //inputFileName = &quot;C:/data/formatConversion/c1002a3T1.hdr&quot;;<br>&nbsp; inputFileName = &quot;C:/data/formatConversion/RPI.mha&quot;;

<br><br>&nbsp; reader-&gt;SetFileName( inputFileName.c_str() );<br><br>&nbsp; /** Generate all information. <br>&nbsp; reader-&gt;GenerateOutputInformation();<br><br>&nbsp; ImageIOBaseType::Pointer testImageIOBase = testReader-&gt;GetImageIO();

<br><br>&nbsp; unsigned int inputDimension = testImageIOBase-&gt;GetNumberOfDimensions();<br>&nbsp; unsigned int numberOfComponents = testImageIOBase-&gt;GetNumberOfComponents();<br>&nbsp; std::string inputPixelComponentType = testImageIOBase-&gt;GetComponentTypeAsString(

<br>&nbsp;&nbsp;&nbsp; testImageIOBase-&gt;GetComponentType() );<br>&nbsp; std::cout&lt;&lt;inputPixelComponentType&lt;&lt;std::endl;<br>&nbsp; std::string pixelType = testImageIOBase-&gt;GetPixelTypeAsString(<br>&nbsp;&nbsp;&nbsp; testImageIOBase-&gt;GetPixelType() );

<br>&nbsp; std::cout&lt;&lt;pixelType&lt;&lt;std::endl;<br><br>&nbsp; std::string&nbsp; outputPixelComponentType = inputPixelComponentType;<br>&nbsp; */<br><br>&nbsp; try <br>&nbsp;&nbsp;&nbsp; {<br>&nbsp;&nbsp;&nbsp; reader -&gt; Update ( ) ;<br>&nbsp;&nbsp;&nbsp; }<br>&nbsp; catch( itk::ExceptionObject&nbsp; &amp;&nbsp; err&nbsp; )

<br>&nbsp;&nbsp;&nbsp; {<br>&nbsp;&nbsp;&nbsp; std::cerr&nbsp; &lt;&lt; &quot;ExceptionObject caught !&quot;&nbsp; &lt;&lt; std::endl;<br>&nbsp;&nbsp;&nbsp; std::cerr&nbsp; &lt;&lt; err &lt;&lt;&nbsp; std::endl;<br>&nbsp;&nbsp;&nbsp; return EXIT_FAILURE;<br>&nbsp;&nbsp;&nbsp; }<br><br>&nbsp; typedef itk::OrientImageFilter&lt;ImageType,ImageType&gt; OrienterType;

<br>&nbsp; OrienterType::Pointer orienter =&nbsp; OrienterType::New();<br>&nbsp; orienter-&gt;UseImageDirectionOn();<br>&nbsp; //orienter-&gt;SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_LPS); <br>&nbsp; orienter-&gt;SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RSA); 

<br>&nbsp; //orienter-&gt;SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RPI); <br>&nbsp; orienter-&gt;SetInput( reader -&gt; GetOutput ( ) );<br>&nbsp; try <br>&nbsp;&nbsp;&nbsp; {<br>&nbsp;&nbsp;&nbsp; orienter-&gt;Update();<br>

&nbsp;&nbsp;&nbsp; }<br>&nbsp; catch( itk::ExceptionObject&nbsp; &amp;&nbsp; err&nbsp; )<br>&nbsp;&nbsp;&nbsp; {<br>&nbsp;&nbsp;&nbsp; std::cerr&nbsp; &lt;&lt; &quot;ExceptionObject caught !&quot;&nbsp; &lt;&lt; std::endl;<br>&nbsp;&nbsp;&nbsp; std::cerr&nbsp; &lt;&lt; err &lt;&lt;&nbsp; std::endl;<br>&nbsp;&nbsp;&nbsp; return EXIT_FAILURE;

<br>&nbsp;&nbsp;&nbsp; }<br><br>&nbsp; typedef itk::ImageFileWriter &lt; ImageType &gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; WriterType;<br><br>&nbsp; WriterType::Pointer writer = WriterType::New();<br><br>&nbsp; itk::NiftiImageIO::Pointer niftIio = itk::NiftiImageIO::New();<br><br>

&nbsp; //writer -&gt; SetImageIO ( niftIio ) ;<br><br>&nbsp; std::string outputFileName; <br><br>&nbsp; outputFileName = &quot;C:/data/formatConversion/RSA.mha&quot;;<br>&nbsp; //outputFileName = &quot;C:/data/formatConversion/LPS.mha&quot;;

<br>&nbsp; //outputFileName = &quot;C:/data/formatConversion/RPI.mha&quot;;<br><br>&nbsp; writer -&gt;SetFileName( outputFileName.c_str() );<br><br>&nbsp; //writer -&gt; SetInput ( reader -&gt; GetOutput ( ) ) ;<br>&nbsp; writer -&gt; SetInput ( orienter -&gt; GetOutput ( ) ) ;

<br><br>&nbsp; writer -&gt; UseCompressionOn ( ) ;<br><br>&nbsp; try <br>&nbsp;&nbsp;&nbsp; {<br>&nbsp;&nbsp;&nbsp; writer -&gt; Update ( ) ;<br>&nbsp;&nbsp;&nbsp; }<br>&nbsp; catch( itk::ExceptionObject&nbsp; &amp;&nbsp; err&nbsp; )<br>&nbsp;&nbsp;&nbsp; {<br>&nbsp;&nbsp;&nbsp; std::cerr&nbsp; &lt;&lt; &quot;ExceptionObject caught !&quot;&nbsp; &lt;&lt; std::endl;

<br>&nbsp;&nbsp;&nbsp; std::cerr&nbsp; &lt;&lt; err &lt;&lt;&nbsp; std::endl;<br>&nbsp;&nbsp;&nbsp; return EXIT_FAILURE;<br>&nbsp;&nbsp;&nbsp; }<br><br>&nbsp; return EXIT_SUCCESS;<br>&nbsp; }<br>