<div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">I only now see that you sent this only to me Cyril! I CC'd Lifan and the list.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Feb 25, 2016 at 11:34 AM, Cyril Jaudet <span dir="ltr"><<a href="mailto:drcjaudet@gmail.com" target="_blank">drcjaudet@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"><div><div><div><div>Hi Lifan, <br></div>here some code that i past in the python interpreter of 3dslicer based on vtk.<br><br>_First download slicer and load multi image module.<br></div>_Import your serie with the dicom importer.<br></div>_Go into the multivolume support/multivolume explorer<br></div>_Enable frame copying or something similar.<br><div><div><div>Now you have two serie (module data to see/rename them)<br></div><div>1 multiframe serie<br></div><div>1 image that will be used as reference to extract the 3d + t image<br></div><div>_Copy/paste the following line in the python interpreter of 3dslicer.<br><br></div><div><br>from __main__ import vtk, qt, ctk, slicer<br>from math import *<br>import numpy as np<br>from vtk.util import numpy_support<br>import SimpleITK as sitk<br>import sitkUtils as su<br>import math<br><br>def convert4Dto3D(multi,reference):<br> multiNode=slicer.util.getNode(multi)<br> refNode=slicer.util.getNode(reference)<br> multiImage=multiNode.GetImageData()<br> N=multiNode.GetNumberOfFrames()<br> for i in range (N): #extract image<br> im=vtk.vtkImageExtractComponents()<br> im.SetInputData(multiImage)<br> im.SetComponents(i)<br> im.Update()<br> frame=slicer.modules.volumes.logic().CloneVolume(slicer.mrmlScene,refNode,'frame_'+str(i))<br> frame.SetAndObserveImageData(im.GetOutput())<br><br><br></div><div>_then type:<br> convert4Dto3D(multi,reference)<br></div><div>changing the name of multi and reference by the corresponding name of your data<br></div><div>_it will extract the image under the name frame0, frame1...<br></div><div>_save them <br><br></div><div>Hope that help,<br></div><div><br>Cyril Jaudet<br></div><div>UZBrussel<br></div></div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2016-02-24 18:46 GMT+01:00 Dženan Zukić <span dir="ltr"><<a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Hi Lifan,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">did you examine the DICOM headers? Do different timepoints have different acquisition times?</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Regards,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Dženan</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Wed, Feb 24, 2016 at 11:22 AM, Chen, Lifan <span dir="ltr"><<a href="mailto:LCHEN41@mgh.harvard.edu" target="_blank">LCHEN41@mgh.harvard.edu</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>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><font size="3">Hey all,</font>
<div><font size="3"><br>
</font></div>
<div><font size="3">Any help would be appreciated. This problem really gets me in for couple of days.</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">Thanks,</font></div>
<div><font size="3">Lifan</font><br>
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>发件人:</b> Chen, Lifan<br>
<b>发送时间:</b> 2016年2月23日 17:48<br>
<b>收件人:</b> <a href="mailto:community@itk.org" target="_blank">community@itk.org</a><br>
<b>主题:</b> ITK try to read 4D dicom time series(3d, t), but get 3d*t<br>
</font><br>
</div><div><div>
<div></div>
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><font size="3">Hi all,</font>
<div><font size="3"><br>
</font></div>
<div><font size="3">These days, I am trying to use ITK to handle 4D dicom series (3d+t). I use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to read these images.</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">The following is part of my code:</font></div>
<div>
<div><font size="3">typedef double PixelType;</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef itk::Image< PixelType, 4> Image4DType; //4D image type</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef itk::Image< PixelType, 3> Image3DType; //3D image type</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef itk::ImageSeriesReader< Image4DType > ReaderType;</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef itk::GDCMImageIO ImageIOType;</font></div>
</div>
<div>
<div><font size="3"><span style="white-space:pre-wrap"></span>reader = ReaderType::New();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>dicomIO = ImageIOType::New();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef itk::GDCMSeriesFileNames NamesGeneratorType;</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>nameGenerator->AddSeriesRestriction("0008|0021");</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>nameGenerator->SetUseSeriesDetails(true);</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>nameGenerator->SetDirectory(_filename);</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef std::vector< std::string > SeriesIdContainer;</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>_isFileLoaded = !(seriesUID.empty());</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>if (true == _isFileLoaded){</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>std::string seriesIdentifier = seriesUID.begin()->c_str();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>typedef std::vector< std::string > FileNamesContainer;</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>FileNamesContainer fileNames;</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>fileNames = nameGenerator->GetFileNames(seriesIdentifier);</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>reader->SetFileNames(fileNames);</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>reader->SetImageIO(dicomIO);</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>reader->Update();</font></div>
<div><font size="3"><span style="white-space:pre-wrap"></span>}</font></div>
</div>
<div><font size="3"><br>
</font></div>
<div><font size="3">I have tried this code and the reader worked well. However I got a [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may caused by nameGenerator, but I use SetUseSeriesDetails and AddSeriesRestriction("0008|0021")(aquisition
time)which are implied by documents to handle 4d images.I have also tried several methods but all not work. I wonder whether ITK have an original method to handle 4d images.</font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">Have anyone ever met this problem before? Any help or recommendations would be appreciated. </font></div>
<div><font size="3"><br>
</font></div>
<div><font size="3">Thanks,</font></div>
<div><font size="3">Lifan</font></div>
</div>
</div>
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