Hi Brad,<br><br>Your suggention works but the when I open this image in a 3D viewer the axial view is with a vertical flip.<br><br>Where did you get the values of Origin and Spacing?<br><br><div>>> joinSeries->SetOrigin(inputOrigin[2]);</div>
<div>>> joinSeries->SetSpacing(inputSpacing[2]);</div><br>I think this is the cause.<br><br>Thanks,<br>Luis<br><br><div class="gmail_quote">On Wed, Apr 29, 2009 at 5:25 PM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="">There is also the JoinSeriesImageFilter. Here is how I have used it before:<div>
<br></div><div><div><br></div><div> typedef itk::JoinSeriesImageFilter<InputImageType, InputVolumeType> JoinSeriesFilterType;</div><div> JoinSeriesFilterType::Pointer joinSeries = JoinSeriesFilterType::New();</div>
<div> joinSeries->SetOrigin(inputOrigin[2]);</div><div> joinSeries->SetSpacing(inputSpacing[2]);</div><div> </div><div><div> for (unsigned int z = 0; z < sliceTransforms.size(); ++z) {</div><div><br></div><div>
</div><div> typedef itk::ExtractImageFilter<InputVolumeType, InputImageType> SlicerExtractorType;</div><div> SlicerExtractorType::Pointer sliceImageExtractor = SlicerExtractorType::New();</div><div> SlicerExtractorType::InputImageRegionType sliceSubRegion(inputVolume->GetLargestPossibleRegion());</div>
<div> sliceSubRegion.SetSize(2, 0);</div><div> sliceSubRegion.SetIndex(2, z); </div><div> sliceImageExtractor->SetExtractionRegion(sliceSubRegion);</div><div> sliceImageExtractor->SetInput(inputVolume); </div>
<div> sliceImageExtractor->Update();</div><div><br></div><div> ... resampling of the slices...</div><div> </div><div> joinSeries->PushBackInput(resample->GetOutput());</div><div> }</div><div> </div>
<div> joinSeries->Update();</div><div><br></div><div><br></div></div><div>Hopefully one of the suggestions will work well for you.</div><div><br></div><div>Brad</div><div><div><div></div><div class="h5"><br><div><div>
On Apr 29, 2009, at 4:13 PM, Bill Lorensen wrote:</div><br><blockquote type="cite"><div>Or you could use itkTileImageFilter. Note the last sentence in the<br>documentation.<br><br>/** \class TileImageFilter<br> * \brief Tile multiple input images into a single output image.<br>
*<br> * This filter will tile multiple images using a user-specified<br> * layout. The tile sizes will be large enough to accommodate the<br> * largest image for each tile. The layout is specified with the<br> * SetLayout method. The layout has the same dimension as the output<br>
* image. If all entries of the layout are positive, the tiled output<br> * will contain the exact number of tiles. If the layout contains a 0<br> * in the last dimension, the filter will compute a size that will<br> * accommodate all of the images. Empty tiles are filled with the<br>
* value specified with the SetDefault value method. The input images<br> * must have a dimension less than or equal to the output image. The<br> * output image have a larger dimension than the input images. This<br> * filter can be used to create a volume from a series of inputs by<br>
* specifying a layout of 1,1,0.<br> */<br><br><br>On Tue, Apr 28, 2009 at 1:41 PM, Luis Ibanez <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>> wrote:<br><blockquote type="cite">
Hi Luis,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">It is a bit more complicated than that.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">You will need to put the filter in a for loop,<br>
</blockquote><blockquote type="cite">where you iterate over all the slices.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Inside the loop you take the output of the<br></blockquote><blockquote type="cite">
PasteImageFilter and reconnect it as a new<br></blockquote><blockquote type="cite">input.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">In Pseudo code it will look something like:<br>
</blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> ImageType::Pointer wholeImage;<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> for-loop<br></blockquote>
<blockquote type="cite"> {<br></blockquote><blockquote type="cite"> pasteFilter->SetInput1( wholeImage );<br></blockquote><blockquote type="cite"> pasteFilter->SetInput2( slice_i );<br></blockquote><blockquote type="cite">
pasteFilter->Update();<br></blockquote><blockquote type="cite"> wholeImage = pasterFilter->GetOutupt();<br></blockquote><blockquote type="cite"> wholeImage->DisconnectPipeline();<br></blockquote><blockquote type="cite">
}<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Regards,<br></blockquote><blockquote type="cite">
<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Luis<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote>
<blockquote type="cite">--------------------------<br></blockquote><blockquote type="cite">Luis Roberto P. Paula wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite">After that, all I need to do is to call the SetInput for each slice and,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">at the end, call the Update method?<br></blockquote>
</blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
Luis<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On Tue, Apr 21, 2009 at 10:06 AM, Luis Ibanez <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>>> wrote:<br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Hi Luis,<br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> You should instantiate the Paste filter in 3D.<br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Since you are going to paste 2D slices into a 3D image,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
you need to set up the filter in such a way that a 2D<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> image is seen as a 3D image of a single slice.<br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"> Regards,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"> Luis<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> -----------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Luis Roberto P. Paula wrote:<br></blockquote>
</blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Hi Luis,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> I'm a little confused on how to use the itkPasteImageFilter.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> At first, I created the typedef:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"> typedef itk::PasteImageFilter< ImageType2D > PasteFilter2D;<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Then:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote>
</blockquote><blockquote type="cite"><blockquote type="cite"> PasteFilter2D::Pointer paste2D = PasteFilter2D::New();<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"> // I'm lost in this part<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
for (int i; i < VECTOR_SIZE; i++) {<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> paste2D->SetInput( IMAGE2D_VECTOR[i] );<br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"> }<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> How do I make the output of the paste2D be a 3D image?<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Do I need to set to the destination image a 3D blank image?<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> The destination index affects the output?<br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> I thought it would work like the add method of the std:vector<br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"> class with an output as a 3D image, but it seems that it can<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> return an image with the same dimension.<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
Luis<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> On Fri, Apr 17, 2009 at 3:36 PM, Luis Ibanez<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>>>> wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Hi Luis,<br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Yes,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> the same should work for pasting 3D images into to 4D images.<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Regards,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Luis<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> ---------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
Luis Roberto P. Paula wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Thanks Luis!! This is a much better approach<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> (itkPasteImageFilter).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"> I guess it works the same way from 3D to 4D, right?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"> Regards,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Luis<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> On Thu, Apr 16, 2009 at 1:59 PM, Luis Ibanez<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>>><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> <<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>>>>> wrote:<br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Hi Luis,<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> If your images are in individual 2D files, then<br></blockquote>
</blockquote><blockquote type="cite"><blockquote type="cite"> you could simply use the ImageSeriesReader.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"> If your images are in an array of 2D images in<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> memory, then you may want to use the Paste<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> filter:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://itk.org/Doxygen/html/itkPasteImageFilter_8h.html" target="_blank">http://itk.org/Doxygen/html/itkPasteImageFilter_8h.html</a><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> You will have to call it multiple times...<br></blockquote>
</blockquote><blockquote type="cite"><blockquote type="cite"> once per input slice.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Regards,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote>
</blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Luis<br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> ---------------------------<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Luis Roberto P. Paula wrote:<br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Hi All,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> I have a set of 2D images in axial orientation and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
I want to<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> create a 3D volume with this images.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> It would be de reverse operation of the class<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
ExtractImageFilter.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Does anybody knows how to do it?<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> Thanks in advance,<br></blockquote></blockquote>
<blockquote type="cite"><blockquote type="cite"> Luis<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">
<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> ------------------------------------------------------------------------<br>
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