[Rtk-users] Error Result by using FDK algorithm to Reconstruction 2D X- ray Scan projection images into 2D CT Slice image

[Simon Rit]

Can you provide the size, origin and spacing of reader->GetOutput()? It's a
bit hard to help you without this information.
Simon

On Thu, Jan 12, 2023 at 11:01 AM 何明哲 <m10512067 at yuntech.org.tw> wrote:

>
> Dear Simon
>
> Thanks for your reply .Its great help for me!
>
> 1.)I was  refer your suggestion and modified the code,
> but the result will be a large blank area and I don't understand why
>
> here is the code and result
>
> sizeOutput[0] = Imagewidth;
>   sizeOutput[1] = 1;
>   sizeOutput[2] = numberOfProjections;
>   spacing[0] = 0.25;
>   spacing[1] = 0.25;
>   spacing[2] = 0.25;
>   origin[0] = (Imagewidth-1)*0.5*spacing[0];
>   origin[1] = (Imageheigh-1)*0.5*spacing[1];
>   origin[2] = spacing[2]*SliceN*-1;
>
>   recoVolume->SetSize(sizeOutput);
>   recoVolume->SetSpacing(spacing);
>   recoVolume->SetOrigin(origin);
>   recoVolume->SetConstant(0.);
>
> [image: image.png]
>
> 2.)if you're doing 2D reconstruction, be careful that your projections
> should not be 1D because the backprojection uses a 2D interpolation. It
> should have at least 2 lines.
>  --> Yes , I hope I can eventually reconstruct a 2D CT Slice, if  my read
> projection step or setting have any problem please let me know,
>
> thanks for your reply
>
> BR,
>
>
>
>
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> 於 2023年1月12日 週四 下午4:30寫道：
>
>> Hi,
>> I'm not sure I have enough information to answer... What I can say is:
>> - that the origin is not set to center your volume, for centering, you
>> should use (size-1)*0.5*spacing
>> - if you're doing 2D reconstruction, be careful that your projections
>> should not be 1D because the backprojection uses a 2D interpolation. It
>> should have at least 2 lines.
>> I hope it helps,
>> Simon
>>
>> On Thu, Jan 12, 2023 at 8:46 AM 何明哲 <m10512067 at yuntech.org.tw> wrote:
>>
>>>
>>> HI Everyone ,
>>>
>>> I have a question
>>> that When I was refer to the official example
>>> "Firstcudareconstruction.cpp",
>>> then I tried to  modify the code and reconstruction 2D x ray projection
>>> image to 2D ct slice,
>>> the code is worked but I got the wrong result too,
>>> I don't understand what the problem I'm have ?
>>>  it's possible that the setting of reconstruction output image size or
>>> origin is wrong?
>>>
>>> here is my code and result (I was tried to only reconstruction just a
>>> slice NO.100 of the whole volume)
>>>
>>>  --------------------------------------------------------------------------------------------
>>>  using GeometryType = rtk::ThreeDCircularProjectionGeometry;
>>>   GeometryType::Pointer geometry = GeometryType::New();
>>>   unsigned int          numberOfProjections = 280;
>>>   double                firstAngle = 0;
>>>   double                angularArc = 280;
>>>   unsigned int          sid = 510;
>>>   unsigned int          sdd = 690;
>>>
>>>   for (unsigned int noProj = 0; noProj < numberOfProjections; noProj++)
>>>   {
>>>     double angle = firstAngle + noProj * angularArc /
>>> numberOfProjections;
>>>     geometry->AddProjection(sid, sdd, angle);
>>>   }
>>>
>>>   rtk::ThreeDCircularProjectionGeometryXMLFileWriter::Pointer xmlWriter;
>>>   xmlWriter = rtk::ThreeDCircularProjectionGeometryXMLFileWriter::New();
>>>   xmlWriter->SetFilename(".\\RTK_Geometry.xml");
>>>   xmlWriter->SetObject(geometry);
>>>   xmlWriter->WriteFile();
>>>
>>>   using NameGeneratorType = itk::NumericSeriesFileNames;
>>>   NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>>>
>>>   nameGenerator->SetSeriesFormat(ProjectionInage +"\\%d.tif");
>>>   nameGenerator->SetStartIndex(1);
>>>   nameGenerator->SetEndIndex(280);
>>>   nameGenerator->SetIncrementIndex(1);
>>>
>>>   using IutputImageType = itk::CudaImage<float, 3>;
>>>   using ReaderType = rtk::ProjectionsReader<IutputImageType>;
>>>   ReaderType::Pointer reader = ReaderType::New();
>>>   reader->SetFileNames(nameGenerator->GetFileNames());
>>>   reader->Update();
>>>
>>>   using ConstantImageSourceType =
>>> rtk::ConstantImageSource<OutputImageType>;
>>>   ConstantImageSourceType::PointType   origin;
>>>   ConstantImageSourceType::SpacingType spacing;
>>>   ConstantImageSourceType::SizeType    sizeOutput;
>>>   ConstantImageSourceType::Pointer     recoVolume =
>>> ConstantImageSourceType::New();
>>>
>>>   sizeOutput[0] = Imagewidth;
>>>   sizeOutput[1] = Imageheigh;
>>>   sizeOutput[2] = numofproj;
>>>   spacing[0] = 0.25;
>>>   spacing[1] = 0.25;
>>>   spacing[2] = 0.25;
>>>   origin[0] = Imagewidth*spacing[0]*0.5*-1;
>>>   origin[1] = Imageheigh*spacing[0]*0.5*-1;
>>>   origin[2] = spacing[2]*SliceN*-1;
>>>
>>>   recoVolume->SetSize(sizeOutput);
>>>   recoVolume->SetSpacing(spacing);
>>>   recoVolume->SetOrigin(origin);
>>>   recoVolume->SetConstant(0);
>>>
>>>   using FDKGPUType = rtk::CudaFDKConeBeamReconstructionFilter;
>>>   FDKGPUType::Pointer feldkamp = FDKGPUType::New();
>>>
>>>   feldkamp->SetInput(0, recoVolume->GetOutput());
>>>   feldkamp->SetInput(1, reader->GetOutput());
>>>   feldkamp->SetGeometry(geometry);
>>>   feldkamp->SetNumberOfThreads(7);
>>>   feldkamp->Update();
>>>
>>>   using WriterType = itk::ImageFileWriter<OutputImageType>;
>>>   WriterType::Pointer writer = WriterType::New();
>>>   writer->SetFileName("C:\\RTK.mhd");
>>>   writer->SetInput(feldkamp->GetOutput());
>>>   writer->Update();
>>>
>>> [image: 20230112_100.PNG]
>>>
>>> it should be look like this
>>> [image: 20230109.PNG]
>>>
>>> thanks for your reply
>>>
>>> BR,
>>>
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> rtk-users at openrtk.org
>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230112/84b106ca/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 20230112_100.PNG
Type: image/png
Size: 104500 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230112/84b106ca/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 20230109.PNG
Type: image/png
Size: 221917 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230112/84b106ca/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 39478 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230112/84b106ca/attachment-0005.png>