<div dir="ltr">From what I read so far, there is a clarification with respect to the difference between the interpretation of the orientation within metaimages files and DICOM images. However, I cannot find clear information on how to tackle the issue of metaimage orientation adjustment.<div>
<br></div><div>Are the answers for the following questions clearly established?:</div><div>1. is the itk::OrientImageFilter fully effective on a metaimage when one desires to change the image orientation both visually and within the stored information?</div>
<div>2. If no, is there a workaround for this problem that allows me to still use metaimages?</div><div>3. Do the ITK registration algorithms, by any chance, match internally the orientations between images?</div><div><br>
</div><div>Thank you for your help!</div><div><br></div><div>Best,</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 29 July 2014 16:53, Andras Lasso <span dir="ltr"><<a href="mailto:lasso@queensu.ca" target="_blank">lasso@queensu.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div dir="ltr" style="font-family:'Calibri','Segoe UI','Meiryo','Microsoft YaHei UI','Microsoft JhengHei UI','Malgun Gothic','sans-serif';font-size:12pt">
<div>We experienced the same issue in Slicer (see <a href="http://www.na-mic.org/Bug/view.php?id=2173" target="_blank">
http://www.na-mic.org/Bug/view.php?id=2173</a>). ITK ignores anatomical orientation in MetaIO images, while ITK properly uses anatomical orientation information in some other file formats (e.g., NRRD).</div>
<div><br>
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<div>Andras<br>
</div>
<div><br>
</div>
<div style="padding-top:5px;border-top-color:rgb(229,229,229);border-top-width:1px;border-top-style:solid">
<div><font face=" 'Calibri', 'Segoe UI', 'Meiryo', 'Microsoft YaHei UI', 'Microsoft JhengHei UI', 'Malgun Gothic', 'sans-serif'" style="line-height:15pt;letter-spacing:0.02em;font-family:"Calibri","Segoe UI","Meiryo","Microsoft YaHei UI","Microsoft JhengHei UI","Malgun Gothic","sans-serif";font-size:12pt"><b>From:</b> <a href="mailto:butlershomecoffee@gmail.com" target="_blank">Butlers
Home</a><br>
<b>Sent:</b> Tuesday, July 29, 2014 10:13 AM<br>
<b>To:</b> <a href="mailto:community@itk.org" target="_blank">community@itk.org</a></font></div>
</div><div><div class="h5">
<div><br>
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<div style="font-family:arial,sans-serif;font-size:13px">I would like to know how I can change the orientation of two 3D images.</div>
<div style="font-family:arial,sans-serif;font-size:13px">Scenario:</div>
<div style="font-family:arial,sans-serif;font-size:13px">- both images are .mha</div>
<div style="font-family:arial,sans-serif;font-size:13px">- one image has RAI as the initial orientation</div>
<div style="font-family:arial,sans-serif;font-size:13px">- 2nd image has LPS as the initial orientation</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">I would like to set the same orientation RAI for both images before processing them (i.e., registering them in my case). With the below mentioned code I manage to change the orientation specified
textually in the .mha files but visually they do not change. Why is that? Is the orientation changing just within the header specifications without actually changing the visualization part? For visualization I used ITK-SNAP.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Here is a code snippet from what I do:</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
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<div style="font-family:arial,sans-serif;font-size:13px">[...]</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">
<div>typedef itk::ImageFileReader< ImageType2 > ImageReaderType1;</div>
<div>typedef itk::ImageFileReader< ImageType1 > ImageReaderType2;</div>
<div><br>
</div>
<div>ImageReaderType1::Pointer imReader1 = ImageReaderType1::New();</div>
<div>ImageReaderType2::Pointer imReader2 = ImageReaderType2::New();</div>
<div><br>
</div>
<div>imReader1->SetFileName("im1.mha");<br>
</div>
<div>imReader2->SetFileName("im2.mha");</div>
<div><br>
</div>
<div>imReader1->Update();</div>
<div><br>
</div>
<div>// set both images to same orientation<br>
</div>
<div><br>
</div>
<div>// orientation filter for 1st image</div>
<div>itk::OrientImageFilter<ImageType1, ImageType1>::Pointer orienter1 = itk::OrientImageFilter<ImageType1, ImageType1>::New();<br>
</div>
<div>orienter1->UseImageDirectionOn();<br>
</div>
<div>orienter1->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);</div>
<div>orienter1->SetInput(imReader1->GetOutput());</div>
<div>orienter1->Update();</div>
<div><br>
</div>
<div>// orientation filter for 2nd image</div>
<div>itk::OrientImageFilter<ImageType2, ImageType2>::Pointer orienter2 = itk::OrientImageFilter<ImageType2, ImageType2>::New();<br>
</div>
<div>orienter2->UseImageDirectionOn();</div>
<div>orienter2->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);</div>
<div>orienter2->SetInput(imReader2->GetOutput());</div>
<div>orienter2->Update();</div>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">[...]</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
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<div style="font-family:arial,sans-serif;font-size:13px">I tried not using the cosine-based approach, i.e., use the itk::AnalyzeImageIO class together with itk::ExposeMetaData<>() but for some unknown reason, the orientation is not determined appropriately.
I would also prefer not using them at all because, as far as I understood, they are deprecated.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Thank you.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Best regards,</div>
<div dir="ltr">--
<div>Butlers</div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>Butlers</div></div>
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