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<p class="MsoNormal">Does Slicer load it correctly as a 4D volume? If yes, you can use that or copy it's behavior on your own software. If Slicer does not load it correctly or you are not sure how to do it, then ask help on the Slicer forum (discourse.slicer.org).</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Andras</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:sonia.pozzi89@gmail.com">Sonia Pozzi</a><br>
<b>Sent: </b>Sunday, July 30, 2017 13:10<br>
<b>To: </b><a href="mailto:lasso@queensu.ca">Andras Lasso</a><br>
<b>Cc: </b><a href="mailto:ljzijp@gmail.com">Lambert Zijp</a>; <a href="mailto:insight-users@itk.org">
Insight-users</a><br>
<b>Subject: </b>Re: [ITK-users] [ITK] Siemens 4d data</p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>Dear Andras and Lambert,
<div class=""><br class="">
</div>
<div class="">here is the code I’m using. Every one of my time series contains the same slice for different times.</div>
<div class=""><br class="">
</div>
<div class="">The problem is that it is importing the series one by one and it seems that it is not working in checking out which slice belong to the same time acquisition.</div>
<div class="">At the end my 4D volume has coordinates [x,y,t,z]. I also tried to switch t- and z-coordinates at the end of my simulation but then I have some problem in the resulting volume (I’m not able to continuing working on it).</div>
<div class="">As you know I can’t share MRI data here, but if you are willing I could send you a small part of them to try to figure out together how to read them...</div>
<div class="">That would help me a lot.</div>
<div class=""><br class="">
</div>
<div class="">Regards and thank you for your time,</div>
<div class=""><br class="">
</div>
<div class="">Sonia</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""> nameGenerator -> SetDirectory( _dicomDirectory );</div>
<div class=""> ReaderType::Pointer reader = ReaderType::New();</div>
<div class=""><br class="">
</div>
<div class=""> ShortImageType4D::Pointer image4D = ShortImageType4D::New();</div>
<div class=""> ShortImageType::Pointer image3D = ShortImageType::New();</div>
<div class=""><br class="">
</div>
<div class=""> reader->SetImageIO(dicomIO);</div>
<div class=""><br class="">
</div>
<div class=""> const std::string entry_id = "0018|1090 ";</div>
<div class=""><br class="">
</div>
<div class=""> nameGenerator->AddSeriesRestriction(entry_id);</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> typedef std::vector< std::string > SeriesIdContainer;</div>
<div class=""> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();</div>
<div class=""> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();</div>
<div class=""> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();</div>
<div class=""><br class="">
</div>
<div class=""> typedef std::vector< std::string > FileNamesContainer;</div>
<div class=""><br class="">
</div>
<div class=""> // figure out how many time points there are based on number of series </div>
<div class=""> unsigned int timepoints = 0;</div>
<div class=""> while (seriesItr != seriesEnd){</div>
<div class=""> timepoints++;</div>
<div class=""> seriesItr++;</div>
<div class=""> }</div>
<div class=""> std::cout << "Number of time points : " << timepoints << std::endl;</div>
<div class=""><br class="">
</div>
<div class=""> seriesItr = seriesUID.begin();</div>
<div class=""> std::cout << "Reading first image : " << std::endl;</div>
<div class=""> std::cout << seriesItr->c_str() << std::endl;</div>
<div class=""><br class="">
</div>
<div class=""> std::string seriesIdentifier;</div>
<div class=""> seriesIdentifier = seriesItr->c_str();</div>
<div class=""><br class="">
</div>
<div class=""> FileNamesContainer fileNames;</div>
<div class=""> fileNames = nameGenerator->GetFileNames(seriesIdentifier);</div>
<div class=""> FileNamesContainer::iterator fileiterator = fileNames.begin();</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> std::cout<<"sono qui"<<seriesIdentifier<<std::endl;</div>
<div class=""><br class="">
</div>
<div class=""> reader->SetFileNames(fileNames);</div>
<div class=""><br class="">
</div>
<div class=""> try</div>
<div class=""> {</div>
<div class=""> reader->Update();</div>
<div class=""> }</div>
<div class=""> catch (itk::ExceptionObject &ex)</div>
<div class=""> {</div>
<div class=""> std::cout << ex << std::endl;</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> const ShortImageType::SpacingType& spacing3D = reader->GetOutput()->GetSpacing();</div>
<div class=""> std::cout << "Spacing 3D = " << spacing3D[0] << ", " << spacing3D[1] << ", " << spacing3D[2] << std::endl;</div>
<div class=""> const ShortImageType::PointType origin3D = reader->GetOutput()->GetOrigin();</div>
<div class=""> std::cout << "Origin 3D = " << origin3D[0] << ", " << origin3D[1] << ", " << origin3D[2] << std::endl;</div>
<div class=""> const ShortImageType::SizeType size3D = reader->GetOutput()->GetBufferedRegion().GetSize();</div>
<div class=""><br class="">
</div>
<div class=""> ShortImageType4D::SpacingType spacing4D;</div>
<div class=""> ShortImageType4D::PointType origin4D;</div>
<div class=""> ShortImageType4D::SizeType size4D;</div>
<div class=""><br class="">
</div>
<div class=""> for (int i = 0; i < 3; ++i){</div>
<div class=""> spacing4D[i] = spacing3D[i];</div>
<div class=""> origin4D[i] = origin3D[i];</div>
<div class=""> size4D[i] = size3D[i];</div>
<div class=""> }</div>
<div class=""> </div>
<div class=""> spacing4D[3] = 1;</div>
<div class=""> origin4D[3] = 0;</div>
<div class=""> size4D[3] = timepoints;</div>
<div class=""><br class="">
</div>
<div class=""> ShortImageType4D::IndexType start4D;</div>
<div class=""> start4D.Fill(0);</div>
<div class=""><br class="">
</div>
<div class=""> ShortImageType4D::RegionType region4D(start4D, size4D);</div>
<div class=""><br class="">
</div>
<div class=""> std::cout << "Spacing 4D = " << spacing4D[0] << ", " << spacing4D[1] << ", " << spacing4D[2] << ", " << spacing4D[3] << std::endl;</div>
<div class=""> std::cout << "Size 4D = " << size4D[0] << ", " << size4D[1] << ", " << size4D[2] << ", " << size4D[3] << std::endl;</div>
<div class=""> image4D->SetRegions(region4D);</div>
<div class=""> image4D->SetSpacing(spacing4D);</div>
<div class=""> image4D->SetOrigin(origin4D);</div>
<div class=""> image4D->Allocate();</div>
<div class=""><br class="">
</div>
<div class=""> seriesItr = seriesUID.begin();</div>
<div class=""><br class="">
</div>
<div class=""> typedef itk::ImageRegionConstIterator< ShortImageType > Iterator3D;</div>
<div class=""> typedef itk::ImageRegionIterator< ShortImageType4D > Iterator4D;</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> Iterator4D it4(image4D, image4D->GetBufferedRegion());</div>
<div class=""> it4.GoToBegin();</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> unsigned short int idx = 0;</div>
<div class=""> while (seriesItr != seriesEnd){</div>
<div class=""><br class="">
</div>
<div class=""> seriesIdentifier = seriesItr->c_str();</div>
<div class=""> std::cout << "Reading series " << std::endl;</div>
<div class=""> std::cout << seriesItr->c_str() << std::endl;</div>
<div class=""><br class="">
</div>
<div class=""> fileNames = nameGenerator->GetFileNames(seriesIdentifier);</div>
<div class=""><br class="">
</div>
<div class=""> for(unsigned int fni = 0; fni<fileNames.size(); fni++)</div>
<div class=""> { std::cout<<"FN "<<fileNames[fni]<<std::endl;</div>
<div class=""><br class="">
</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""> reader->SetFileNames(fileNames);</div>
<div class=""><br class="">
</div>
<div class=""> image3D = reader->GetOutput();</div>
<div class=""> image3D->SetRegions(reader->GetOutput()->GetRequestedRegion());</div>
<div class=""> image3D->CopyInformation(reader->GetOutput());</div>
<div class=""> image3D->Allocate();</div>
<div class=""><br class="">
</div>
<div class=""> std::cout << "reading image volume " << idx << std::endl << std::endl;</div>
<div class=""> try</div>
<div class=""> {</div>
<div class=""> reader->Update();</div>
<div class=""> }</div>
<div class=""> catch (itk::ExceptionObject &ex)</div>
<div class=""> {</div>
<div class=""> std::cout << ex << std::endl;</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> </div>
<div class=""> Iterator3D it3(image3D, image3D->GetBufferedRegion());</div>
<div class=""> it3.GoToBegin();</div>
<div class=""><br class="">
</div>
<div class=""> while (!it3.IsAtEnd())</div>
<div class=""> {</div>
<div class=""> it4.Set(it3.Get());</div>
<div class=""> ++it3;</div>
<div class=""> ++it4;</div>
<div class=""> }</div>
<div class=""><br class="">
</div>
<div class=""> // increment iterator</div>
<div class=""> seriesItr++; </div>
<div class=""> idx++;</div>
<div class=""><br class="">
</div>
<div class=""> }</div>
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 29 Jul 2017, at 20:58, Andras Lasso <<a href="mailto:lasso@queensu.ca" class="">lasso@queensu.ca</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Finding out what DICOM fields to use for grouping frames is a complex topic. There is no universally accepted standard, the field(s) to use depend on scanner manufacturer, imaging modality, and imaging protocol.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
You can have a look at the 4D image importer logic in 3D Slicer (what DICOM fields are considered, what heuristics are used for automatically detecting special cases, etc):<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffedorov%2FMultiVolumeImporter%2Fblob%2Fmaster%2FMultiVolumeImporterPlugin.py&data=02%7C01%7Classo%40queensu.ca%7C2c8ee4263d3e4bc7852e08d4d76dcf42%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636370314013534944&sdata=TSgfUbldP6g%2ByIXlxlKKTog3wDo95QduwU9YAut52A4%3D&reserved=0" style="color: purple; text-decoration: underline;" class="">https://github.com/fedorov/MultiVolumeImporter/blob/master/MultiVolumeImporterPlugin.py</a><o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
You may also consider using 3D Slicer for loading DICOM data and saving as a 4D nrrd file that you can then easily load into ITK. If you have any questions related to this then post it on<span class="Apple-converted-space"> </span><a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.slicer.org%2F&data=02%7C01%7Classo%40queensu.ca%7C2c8ee4263d3e4bc7852e08d4d76dcf42%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636370314013534944&sdata=RIwlK%2BCGepL9Fd5q4NvhCoZAq6qCe7Uyay1%2FBH%2B8hVA%3D&reserved=0" style="color: purple; text-decoration: underline;" class="">https://discourse.slicer.org</a>.<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Andras<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<a name="_MailEndCompose" class=""><o:p class=""> </o:p></a></div>
<span class=""></span>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class="">From:</b><span class="Apple-converted-space"> </span>Community [<a href="mailto:community-bounces@itk.org" class="">mailto:community-bounces@itk.org</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Lambert
Zijp<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, July 29, 2017 1:38 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Sonia Pozzi <<a href="mailto:sonia.pozzi89@gmail.com" class="">sonia.pozzi89@gmail.com</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Insight-users <<a href="mailto:insight-users@itk.org" class="">insight-users@itk.org</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ITK] [ITK-users] Siemens 4d data<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hi Sonia,<o:p class=""></o:p></div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Apparently SeriesInstanceUID does not help; sounds familiar. Maybe FrameNumber, SeriesNumber or AcquisitionNumber? If not, sorting slices on slice coordinate and AcquisitionTime could be done as a last resort. If you post two slices with the same coordinate
but belonging to different volumes, I will take look at it.<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Greetings, Lambert<o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
On Sat, Jul 29, 2017 at 12:26 AM, Sonia Pozzi <<a href="mailto:sonia.pozzi89@gmail.com" target="_blank" style="color: purple; text-decoration: underline;" class="">sonia.pozzi89@gmail.com</a>> wrote:<o:p class=""></o:p></div>
<blockquote style="border-style: none none none solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;" class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hello,<br class="">
<br class="">
I have a set of Siemens series. In each series there is the same slice for different times.<br class="">
I would like to be able to reconstruct in itk each single volume (a complete volume for every time step).<br class="">
It is a couple of week that I’m trying how to do that…<br class="">
I understood that I should use some tag, but I’m not sure about which and my code is not working.<br class="">
<br class="">
Could you be so kind to give me a suggestion here?<br class="">
<br class="">
My regards,<br class="">
<br class="">
Sonia<br class="">
_____________________________________<br class="">
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