[Rtk-users] Error Result by using FDK algorithm to Reconstruction 2D X- ray Scan projection images into 2D CT Slice image
何明哲
m10512067 at yuntech.org.tw
Fri Jan 13 09:29:44 CET 2023
Hi Simon
Sure, here is those information for reader->Getoutput()
Size(XYZ)-> 1152,1152,270
Spacing(XYZ)-> 0.25,025,0.25.
Origin(XYZ)-> 143.875,143.875,143.875
but your suggestion inspires me a lot ,
I was use add TiffimageIO to set size spacing origin to projectionreader
source
finally ,I can get this (see attached file )
Although the image still has a lot of artifact and is not clear enough,
Did you have any suggestion for this?
but finally it is a huge breakthrough for me
thanks for help and reply again
Simon Rit <simon.rit at creatis.insa-lyon.fr> 於 2023年1月12日 週四 下午10:57寫道：
> 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
>>>>
>>>
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