<div dir="ltr">Found recorded bugs related to this:<div><br></div><div><a href="https://issues.itk.org/jira/browse/ITK-3176">https://issues.itk.org/jira/browse/ITK-3176</a> (spacing)<br></div><div><a href="https://issues.itk.org/jira/browse/ITK-3407">https://issues.itk.org/jira/browse/ITK-3407</a> (origin)<br></div><div><br></div><div>Guess we wait and watch.</div><div><br></div><div>Thanks a ton for your help,</div><div>Sarthak </div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 9, 2017 at 10:26 AM, Sarthak P <span dir="ltr"><<a href="mailto:scapegoat.sarthak@gmail.com" target="_blank">scapegoat.sarthak@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">So the thing is that even the origin isn't picked up when reading the DICOM image (it is always 0,0,0) so I am guessing I am doing something wrong when writing into the tag 0020|0032 itself. Once that is rectified, the spacing information (should) correct itself.<div><br></div><div>Best,</div><div>Sarthak <div><div class="h5"><br><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 9, 2017 at 10:25 AM, Sarthak P <span dir="ltr"><<a href="mailto:scapegoat.sarthak@gmail.com" target="_blank">scapegoat.sarthak@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">Hi Matt,<div><br></div><div>Yes I do know that. I have tried to put the spacing information from the itk::Image using various combinations with the tags 0018|0088 (slice thickness) and 0018|0050 (spacing between slices) but to no avail.</div><div><br></div><div>Thanks for your help,</div><div>Sarthak </div><div><div class="m_-4782107758148248230h5"><div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Mar 9, 2017 at 9:47 AM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">HI Sarthak,<br>
<br>
The slice thickness is different from the spacing between slices. In<br>
DICOM, slice thickness is related to the point spread function of the<br>
imaging system and slice spacing is related to digital sampling.<br>
<br>
Hope this helps,<br>
Matt<br>
<div class="m_-4782107758148248230m_-10176136869495535gmail-HOEnZb"><div class="m_-4782107758148248230m_-10176136869495535gmail-h5"><br>
On Thu, Mar 9, 2017 at 9:30 AM, Sarthak P <<a href="mailto:scapegoat.sarthak@gmail.com" target="_blank">scapegoat.sarthak@gmail.com</a>> wrote:<br>
> Hi Matt,<br>
><br>
> Thanks for the response.<br>
><br>
> I don't think I am having issues with writing into the tags since I am able<br>
> to read the correct information I am writing (for instance, the tag<br>
> "0020|0032" is always populated with the physical coordinate of the specific<br>
> slice in a correct manner both during writing and reading). In an example,<br>
> the slice thickness should be "2" and the separation between the dicom<br>
> slices is "2", which is correct. But when ITK is reading this collection, it<br>
> keeps the slice thickness at "1". I am seeing the same behavior in other<br>
> applications as well (ITK-SNAP, etc.).<br>
><br>
> Could there be some tag I am missing to write? Since my last post, I tried<br>
> writing only to the tag "0020|0032"; the output dictionary array gets<br>
> populated properly but the file is still not written as expected. I am using<br>
> ITK 4.11, BTW.<br>
><br>
> Best,<br>
> Sarthak<br>
><br>
> On Thu, Mar 9, 2017 at 9:20 AM, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>><br>
> wrote:<br>
>><br>
>> Hi Sarthak,<br>
>><br>
>> DICOM export requires improved typing to produce a valid set of tags.<br>
>> This work has been started here:<br>
>><br>
>> <a href="https://github.com/KitwareMedical/ITKDICOM" rel="noreferrer" target="_blank">https://github.com/KitwareMed<wbr>ical/ITKDICOM</a><br>
>><br>
>> but the implementation is in initial stages. I would be happy to<br>
>> provide guidance if you would like to move it forward.<br>
>><br>
>> Thanks,<br>
>> Matt<br>
>><br>
>> On Wed, Mar 8, 2017 at 3:11 PM, Sarthak P <<a href="mailto:scapegoat.sarthak@gmail.com" target="_blank">scapegoat.sarthak@gmail.com</a>><br>
>> wrote:<br>
>> > Hello All,<br>
>> ><br>
>> > I am trying to write a DICOM image but I want to preserve the properties<br>
>> > from the input image (origin, direction, spacing, etc.). The ITK<br>
>> > examples do<br>
>> > not show how to do this properly and anything I have done with the dicom<br>
>> > tags hasn't worked. Any help would be much appreciated.<br>
>> ><br>
>> > Here is what I have so far:<br>
>> ><br>
>> > //////////<br>
>> > const std::string dataDir = argv[1];<br>
>> > const std::string inputFile = dataDir + "/inputImage.nii.gz";<br>
>> > const std::string outputDir = dataDir + "/test/";<br>
>> ><br>
>> > using ImageTypeToRead = itk::Image< float, 3 >;<br>
>> > using ImageTypeToWrite = itk::Image< short, 3 >;<br>
>> > auto inputImage = cbica::ReadImageWithOrientFix< itk::Image< float, 3<br>
>> > ><br>
>> >>(inputFile);<br>
>> > auto imageToWrite = inputImage;<br>
>> ><br>
>> > auto dicomIO = itk::GDCMImageIO::New();<br>
>> ><br>
>> > auto seriesWriter = itk::ImageSeriesWriter< ImageTypeToWrite,<br>
>> > itk::Image<ImageTypeToWrite::P<wbr>ixelType, 2> >::New();<br>
>> ><br>
>> > auto namesGenerator = itk::NumericSeriesFileNames::N<wbr>ew();<br>
>> > auto start = imageToWrite->GetLargestPossib<wbr>leRegion().GetIndex();<br>
>> > auto size = imageToWrite->GetLargestPossib<wbr>leRegion().GetSize();<br>
>> > namesGenerator->SetSeriesForm<wbr>at((outputDir +<br>
>> > "/image%03d.dcm").c_str());<br>
>> > namesGenerator->SetStartIndex<wbr>(start[2]);<br>
>> > namesGenerator->SetEndIndex(s<wbr>tart[2] + size[2] - 1);<br>
>> > namesGenerator->SetIncrementI<wbr>ndex(1);<br>
>> ><br>
>> > auto castFilter = itk::CastImageFilter<ImageType<wbr>ToRead,<br>
>> > ImageTypeToWrite>::New();<br>
>> > castFilter->SetInput(imageToW<wbr>rite);<br>
>> > castFilter->Update();<br>
>> ><br>
>> > seriesWriter->SetInput(castFi<wbr>lter->GetOutput());<br>
>> > seriesWriter->SetImageIO(dico<wbr>mIO);<br>
>> > seriesWriter->SetFileNames(na<wbr>mesGenerator->GetFileNames());<br>
>> ><br>
>> > typename itk::ImageSeriesReader< ImageTypeToRead<br>
>> > >::DictionaryArrayType<br>
>> > outputArray;<br>
>> ><br>
>> > // this doesn't work at all - was kind of hoping it would do the heavy<br>
>> > lifting for me<br>
>> > //dicomIO->SetOrigin(0, imageToWrite->GetOrigin()[0]);<br>
>> > //dicomIO->SetOrigin(1, imageToWrite->GetOrigin()[1]);<br>
>> > //dicomIO->SetOrigin(2, imageToWrite->GetOrigin()[2]);<br>
>> > //dicomIO->SetSpacing(0, imageToWrite->GetSpacing()[0])<wbr>;<br>
>> > //dicomIO->SetSpacing(1, imageToWrite->GetSpacing()[1])<wbr>;<br>
>> > //dicomIO->SetSpacing(2, imageToWrite->GetSpacing()[2])<wbr>;<br>
>> > //dicomIO->SetDimensions(0,<br>
>> > imageToWrite->GetLargestPossib<wbr>leRegion().GetSize()[0]);<br>
>> > //dicomIO->SetDimensions(1,<br>
>> > imageToWrite->GetLargestPossib<wbr>leRegion().GetSize()[1]);<br>
>> > //dicomIO->SetDimensions(2,<br>
>> > imageToWrite->GetLargestPossib<wbr>leRegion().GetSize()[2]);<br>
>> > // this doesn't work at all<br>
>> ><br>
>> > for (size_t i = 0; i <<br>
>> > imageToWrite->GetLargestPossib<wbr>leRegion().GetSize()[2]; i++)<br>
>> > {<br>
>> > auto dict = new itk::ImageSeriesReader< ImageTypeToRead<br>
>> >>::DictionaryType;<br>
>> > typename ImageTypeToWrite::PointType position;<br>
>> > typename ImageTypeToWrite::IndexType index;<br>
>> > index[0] = 0;<br>
>> > index[1] = 0;<br>
>> > index[2] = i;<br>
>> > imageToWrite->TransformIndexT<wbr>oPhysicalPoint(index, position);<br>
>> > // tags extracted from dicom lookup<br>
>> > <a href="http://dicomlookup.com/lookup.asp" rel="noreferrer" target="_blank">http://dicomlookup.com/lookup.<wbr>asp</a><br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0020|0032",<br>
>> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) + "\\"<br>
>> > +<br>
>> > std::to_string(position[2])); // patient position<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0018|5100",<br>
>> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) + "\\"<br>
>> > +<br>
>> > std::to_string(position[2]));<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "2020|0010",<br>
>> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) + "\\"<br>
>> > +<br>
>> > std::to_string(position[2]));<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0018|5101",<br>
>> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) + "\\"<br>
>> > +<br>
>> > std::to_string(position[2]));<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0018|0050",<br>
>> > std::to_string(imageToWrite->G<wbr>etSpacing()[2])); // Slice Thickness<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0018|0088",<br>
>> > std::to_string(imageToWrite->G<wbr>etSpacing()[2])); // Spacing Between<br>
>> > Slices<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0008|0008",<br>
>> > "DERIVED\\SECONDARY"); // Image Type<br>
>> > itk::EncapsulateMetaData<std:<wbr>:string>(*dict, "0008|0064", "DV"); //<br>
>> > Conversion Type<br>
>> ><br>
>> > outputArray.push_back(dict);<br>
>> > }<br>
>> ><br>
>> > seriesWriter->SetMetaDataDict<wbr>ionaryArray(&outputArray); // no<br>
>> > dictionary<br>
>> > information present without seriesReader<br>
>> ><br>
>> > try<br>
>> > {<br>
>> > seriesWriter->Write();<br>
>> > }<br>
>> > catch (itk::ExceptionObject &e)<br>
>> > {<br>
>> > std::cerr << "Error occurred while trying to write the image '" <<<br>
>> > outputDir << "': " << e.what() << "\n";<br>
>> > exit(EXIT_FAILURE);<br>
>> > }<br>
>> ><br>
>> > //////////<br>
>> ><br>
>> > Thanks a ton,<br>
>> > Sarthak<br>
>> ><br>
>> > ______________________________<wbr>_______<br>
>> > Powered by <a href="http://www.kitware.com" rel="noreferrer" target="_blank">www.kitware.com</a><br>
>> ><br>
>> > Visit other Kitware open-source projects at<br>
>> > <a href="http://www.kitware.com/opensource/opensource.html" rel="noreferrer" target="_blank">http://www.kitware.com/opensou<wbr>rce/opensource.html</a><br>
>> ><br>
>> > Kitware offers ITK Training Courses, for more information visit:<br>
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>> ><br>
>> > Please keep messages on-topic and check the ITK FAQ at:<br>
>> > <a href="http://www.itk.org/Wiki/ITK_FAQ" rel="noreferrer" target="_blank">http://www.itk.org/Wiki/ITK_FA<wbr>Q</a><br>
>> ><br>
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>> ><br>
><br>
><br>
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