Thanks everyone!! I&#39;m gonna try your suggestions.<br><br>Regards,<br>Luis<br><br><div class="gmail_quote">On Wed, Apr 29, 2009 at 5:25 PM, Bradley Lowekamp <span dir="ltr">&lt;<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>&gt;</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&lt;InputImageType, InputVolumeType&gt; JoinSeriesFilterType;</div><div>  JoinSeriesFilterType::Pointer joinSeries = JoinSeriesFilterType::New();</div>
<div>  joinSeries-&gt;SetOrigin(inputOrigin[2]);</div><div>  joinSeries-&gt;SetSpacing(inputSpacing[2]);</div><div>  </div><div><div>  for (unsigned int z = 0; z &lt; sliceTransforms.size(); ++z) {</div><div><br></div><div>
    </div><div>    typedef itk::ExtractImageFilter&lt;InputVolumeType, InputImageType&gt; SlicerExtractorType;</div><div>    SlicerExtractorType::Pointer sliceImageExtractor = SlicerExtractorType::New();</div><div>    SlicerExtractorType::InputImageRegionType sliceSubRegion(inputVolume-&gt;GetLargestPossibleRegion());</div>
<div>    sliceSubRegion.SetSize(2, 0);</div><div>    sliceSubRegion.SetIndex(2, z);    </div><div>    sliceImageExtractor-&gt;SetExtractionRegion(sliceSubRegion);</div><div>    sliceImageExtractor-&gt;SetInput(inputVolume); </div>
<div>    sliceImageExtractor-&gt;Update();</div><div><br></div><div>    ... resampling of the slices...</div><div>      </div><div>    joinSeries-&gt;PushBackInput(resample-&gt;GetOutput());</div><div>  }</div><div>    </div>
<div>  joinSeries-&gt;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 &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>&gt; 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-&gt;SetInput1( wholeImage );<br></blockquote><blockquote type="cite">     pasteFilter-&gt;SetInput2( slice_i );<br></blockquote><blockquote type="cite">
     pasteFilter-&gt;Update();<br></blockquote><blockquote type="cite">     wholeImage = pasterFilter-&gt;GetOutupt();<br></blockquote><blockquote type="cite">     wholeImage-&gt;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 &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite">&lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;&gt; 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&#39;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&lt; ImageType2D &gt; 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&#39;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 &lt; VECTOR_SIZE; i++) {<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">            paste2D-&gt;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">       &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a> &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite">       &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite">       &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;&gt;&gt; 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">              &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a> &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite">       &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a> &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;&gt;<br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite">              &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a><br></blockquote></blockquote><blockquote type="cite">
<blockquote type="cite">       &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">              &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a><br>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite">       &lt;<a href="mailto:luis.ibanez@kitware.com" target="_blank">mailto:luis.ibanez@kitware.com</a>&gt;&gt;&gt;&gt; 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>
</blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">                     _____________________________________<br></blockquote>
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<div> <span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style="">
<span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><p style="margin: 0px;">
<font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="3">========================================================</font></p>
<p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="3">Bradley Lowekamp<span> </span><span> </span></font></p>
<p style="margin: 0px;"><font face="Arial"><span style="font-family: Arial;"><span style="font-family: Arial;">Lockheed Martin </span></span></font><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="3">Contractor for</font></p>
<p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="3">Office of High Performance Computing and Communications</font></p>
<p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="3">National Library of Medicine<span> </span></font></p>
<p style="margin: 0px;"><font style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;" face="Helvetica" size="3"><a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a></font></p>
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