[vtkusers] (dcmtk -> vtkImageData) for Volume rendering

Wed Feb 10 09:34:06 EST 2016

Hello Mallikarjun,

If it is a CT scan, maybe you're missing the Rescale Intercept Slope
parameters to get the same results as the vtkDicomImageReader ?
https://blog.kitware.com/dicom-rescale-intercept-rescale-slope-and-itk/

Simon

2016-02-10 15:12 GMT+01:00 Mallikarjun K <mallikarjun49 at gmail.com>:

> Hello Cory,
>
> Yes,the first image looks like a human head but it is surrounded by some
> other gray/balck colored stuff.I think you are right,it is the issue with
> color/opacity maps.The data is in the range of 0-65536(unsigned short).
> Below are the color and opacity maps I applied.
>
>                 //setup opacity
> d->m_opacityTransferFunction->AddPoint(132.108911, 0.000000);
> d->m_opacityTransferFunction->AddPoint(197.063492, 0.041333);
> d->m_opacityTransferFunction->AddPoint(1087.917989, 0.700000);
> //setup gradient opacity
> d->m_gradientTransferFunction->AddPoint(560.695000, 1.000000);
>
> // Setup color
> d->m_colorTransferFunction->AddRGBPoint(176.881890, 0.650980, 0.000000,
> 0.000000);
> d->m_colorTransferFunction->AddRGBPoint(239.427822, 0.933333, 0.000000,
> 0.000000);
> d->m_colorTransferFunction->AddRGBPoint(301.973753, 1.000000, 0.800000,
> 0.062745);
> d->m_colorTransferFunction->AddRGBPoint(495.866142, 1.000000, 0.905882,
> 0.666667);
> d->m_colorTransferFunction->AddRGBPoint(677.249344, 1.000000, 0.882353,
> 0.215686);
> d->m_colorTransferFunction->AddRGBPoint(808.595801, 1.000000, 1.000000,
> 1.000000);
>
> What should I do to eliminate gray/balck colored stuff ? please guide me.
>
> Thank you.
> Regards,
> Mallikarjun
>
>
>
> On Wed, Feb 10, 2016 at 7:18 PM, Cory Quammen <cory.quammen at kitware.com>
> wrote:
>
>> Mallikarjun,
>>
>> Could you clarify for me whether the first image at all looks like a
>> human head? Is the issue that the color/opacity maps do not appear to be
>> applied correctly, or that the data is just completely strange when reading
>> from dcmtk?
>>
>> If it is the latter, I have a couple guesses:
>>
>> - maybe your dimensions are off from what dcmtk tells you
>> - maybe dcmtk's conventions for voxel order are different from VTK
>>
>> Cory
>>
>> On Wed, Feb 10, 2016 at 2:40 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>> wrote:
>>
>>> Hello Cory Quammen,
>>>
>>> Thanks for the response and suggestions.We are kind of established in
>>> using dcmtk in our project,So couldn't use vtk-dicom for time being.
>>>
>>> Below is the code snippet which I used to get dcmtk data to vtk:
>>>
>>>
>>> vtkDataArray* scalars = 0;
>>>
>>>
>>>
>>> switch (dicomDataType)
>>> {
>>> case TYPE_U32Data:
>>> scalars = vtkUnsignedIntArray::New();
>>> ((vtkUnsignedIntArray*)(scalars))->SetArray((unsigned int*)dicomData,
>>> dicomDataSize, 1);//dicomData is the data from dcmtk
>>> break;
>>> case TYPE_U8Data:
>>> scalars = vtkUnsignedCharArray::New();
>>> ((vtkUnsignedCharArray*)(scalars))->SetArray((unsigned char*)dicomData,
>>> dicomDataSize, 1);
>>> break;
>>> case TYPE_U16Data:
>>> scalars = vtkUnsignedShortArray::New();
>>> ((vtkUnsignedShortArray*)(scalars))->SetArray((unsigned
>>> short*)dicomData, dicomDataSize, 1);
>>> break;
>>> case TYPE_S16Data:
>>> scalars = vtkShortArray::New();
>>> ((vtkShortArray*)(scalars))->SetArray((short*)dicomData, dicomDataSize,
>>> 1);
>>> break;
>>> }
>>> scalars->SetNumberOfComponents(1);
>>> double range[2];
>>> scalars->GetRange(range);
>>> m_imageData = vtkImageData::New();
>>> m_imageData->SetDimensions(dimensions);
>>> m_imageData->SetSpacing(spacing);
>>> m_imageData->GetPointData()->SetScalars(scalars);
>>> scalars->Delete();
>>> m_imageData->GetPointData()->GetScalars()->SetName("VR Cuboid");
>>>
>>>
>>> Thanks&Regards,
>>> Mallikarjun
>>>
>>>
>>>
>>> On Tue, Feb 9, 2016 at 8:47 PM, Cory Quammen <cory.quammen at kitware.com>
>>> wrote:
>>>
>>>> How are you getting the data from dcmtk to VTK? Code would be helpful.
>>>>
>>>> As an aside, you may be interested in David Gobbi's excellent DICOM
>>>> reader for VTK.
>>>>
>>>> https://github.com/dgobbi/vtk-dicom
>>>>
>>>> I believe you can build this within VTK by enabling the Module_vtkDICOM
>>>> option.
>>>>
>>>> Best,
>>>> Cory
>>>>
>>>> On Tue, Feb 9, 2016 at 8:25 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>>>> wrote:
>>>>
>>>>> Hello All,
>>>>> I used dcmtk to read dicom raw data and applied Modality LUT and
>>>>> created a vtkImageData. When I used this data for Volume
>>>>> Rendering(vtkGPUVolumeRayCastMapper), I am getting the following output.
>>>>>
>>>>>
>>>>> [image: Inline image 2]
>>>>>
>>>>>
>>>>> When I used vtkDicomImageReader's output for Volume rendering ,I am
>>>>> getting the following output.
>>>>>
>>>>> [image: Inline image 1]
>>>>>
>>>>> Can anyone give some pointers why this is happening?
>>>>>
>>>>> Thanks in advance..
>>>>> --
>>>>> *With Kind Regards:*
>>>>> Mallikarjun
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Please keep messages on-topic and check the VTK FAQ at:
>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>
>>>>> Search the list archives at: http://markmail.org/search/?q=vtkusers
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Cory Quammen
>>>> R&D Engineer
>>>> Kitware, Inc.
>>>>
>>>
>>>
>>>
>>> --
>>> *With Kind Regards:*
>>> Mallikarjuna K,
>>> 07795531103/09908238861.
>>>
>>>
>>
>>
>> --
>> Cory Quammen
>> R&D Engineer
>> Kitware, Inc.
>>
>
>
>
> --
> *With Kind Regards:*
> Mallikarjuna K,
> 07795531103/09908238861.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
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>
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>

-- 
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Simon Esneault
Rennes, France
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