<div dir="ltr">Thanks for the guide.<div><br></div><div>Best,</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 17 March 2014 18:59, Luis Ibanez <span dir="ltr"><<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Guillaume,<div><br></div><div>Yes, using the GDCM classes in ITK, for processing all the DICOM series (both for reading and writing) will be a good way of enforcing consistency on the management of the coordinate systems.</div>
<div><br></div><div> Regards,</div><div><br></div><div> Luis</div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 17, 2014 at 11:59 AM, Guillaume Lemaître <span dir="ltr"><<a href="mailto:g.lemaitre58@gmail.com" target="_blank">g.lemaitre58@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks Luis,<div><br></div><div>I didn't think yet about suggestion A) and it solves already one of the issue that I observed.</div>
<div><br></div><div>Regarding the other orientation problem, I think I see the problem more clearly. The relevant thing that I didn't consider at first is:</div>
<div><ol type="1" style="line-height:22px;font-size:12px;font-family:'Lucida Grande',Verdana,Geneva,Arial,sans-serif"><li>Extract <a href="http://www.itk.org/Doxygen/html/classitk_1_1Image.html" title="Templated n-dimensional image class. " style="color:rgb(70,101,162);font-weight:bold" target="_blank">Image</a> Orientation & <a href="http://www.itk.org/Doxygen/html/classitk_1_1Image.html" title="Templated n-dimensional image class. " style="color:rgb(70,101,162);font-weight:bold" target="_blank">Image</a> Position from DICOM images, and then calculate the ordering based on the 3D coordinate of the slice</li>
</ol></div><div>And I saw that the last image in the serie becomes the origin so it should be something related with the acquisition performed in the "reverse way" when considering the 3D coordinates.</div><div>
Probably, I could start by receiving all the series using GDCM, which would avoid any trouble with the header after.</div><div><br></div><div>Thanks,</div><div><br></div><div>Best regards,</div></div><div>
<div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 17 March 2014 16:36, Luis Ibanez <span dir="ltr"><<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Guillaume,<div><br></div><div><br></div><div>Thanks for the detailed description of what you are trying to do.</div><div><br></div><div><br></div><div>A) When resampling an image mask, please make sure to use the </div>
<div><br></div><div> NearestNeighbor interpolator,</div><div><br></div><div> so that the values of the mask are not blended in the borders.</div><div><br></div><div><br></div><div>B) Your expectation on the behavior of the origin is correct.</div>
<div><br></div><div> You are correctly feeding to the ResampleImageFilter the</div><div> parameters of the target image:</div><div><br></div><div> Origin</div><div> Spacing<br></div><div> Direction<br>
</div><div> Size<br></div><div><br></div><div>C) Make sure that the "targetVolume" source of the image</div><div> has been updated BEFORE you take the values from</div><div> it output. That is, if the targetVolume class is a file reader,</div>
<div> then you may want to do something like:</div><div><br></div><div> targetVolume->Update();</div><div> const TargetImageType * targetImage = targetVolume->GetOutput();</div><div><br></div><div><div style="font-family:arial,sans-serif;font-size:13px">
<div> resampler->SetOutputOrigin( targetImage->GetOrigin() );</div><div> resampler->SetOutputSpacing( targetImage->GetSpacing() );</div><div> resampler->SetOutputDirection( targetImage->GetOutput()->GetDirection() );</div>
<div> resampler->SetSize( targetImage->GetLargestPossibleRegion().GetSize() );</div><div><br></div><div> resampler->Update();</div><div><br></div><div><br></div><div>D) At the moment of registering, what really matters is the Origin value</div>
<div> inside ITK, regardless of whether it matches the one in the DICOM tags.</div><div><br></div><div>E) At the moment of saving the resampled mask into a DICOM file(s),</div><div> you can then cross check whether the origin tags in the resampled</div>
<div> mask DICOM file, matches the ones from the targetVolume DICOM files.<br><br></div><div> That is, give ITK and GDCM the opportunity to the the proper magic</div><div> in the process of reading and writing the image.</div>
<div><br></div><div><br></div><div>Please let us know if you run into any questions, as you do this.</div><div><br></div><div><br></div><div> Thanks</div><div><br></div><div><br></div><div> Luis</div><div><br></div>
<div> </div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Mon, Mar 17, 2014 at 7:38 AM, Guillaume Lemaître <span dir="ltr"><<a href="mailto:g.lemaitre58@gmail.com" target="_blank">g.lemaitre58@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi all,<div><br></div><div>I am currently working on the following task. I got two DICOM series from different modality with different spacing, and origin. A third DICOM serie correspond to binary segmentation of one the previous serie. I would like to "project" this segmentation into the other serie. I think that the resampling filter should make this work quite well. It should look something like that:</div>
<div><br></div><div><div> ResampleFilterType::Pointer resampler = ResampleFilterType::New();</div><div> resampler->SetInput( maskVolume->GetOutput() );</div><div> resampler->SetTransform( transform );</div><div>
resampler->SetInterpolator( interpolator );</div><div> resampler->SetOutputOrigin( targetVolume->GetOutput()->GetOrigin() );</div><div> resampler->SetOutputSpacing( targetVolume->GetOutput()->GetSpacing() );</div>
<div> resampler->SetOutputDirection( targetVolume->GetOutput()->GetDirection() );</div><div> resampler->SetSize( targetVolume->GetOutput()->GetLargestPossibleRegion().GetSize() );</div><div> resampler->Update();</div>
</div><div><br></div><div>However, I got trapped with what seems to be a problem of origin. I search around and different discussions and got quite confused. From what I found is the following:</div><div>Using gdcminfo to read the origin of targetVolume will give me the same information than the tag (0020,0032) of the DICOM header. However, it will be different from targetVolume->GetOuput()->GetOrigin() which imply a shift when saving my data later.</div>
<div><br></div><div>What should the proper way to do such task?<br clear="all"><div><br></div><div>Thanks in advance,</div><div><br></div><div>Best regards,</div>-- <br><div dir="ltr"><div><span style="font-family:'Times New Roman';font-size:medium"><table style="width:638px" border="0" cellpadding="0">
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