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

Wed Feb 10 11:56:10 EST 2016

Hello Simon and Cory,
As I said in my first post,I applied ModalityLUT(which is nothing but
applying rescale slope and rescale intercept ) on dicom raw data of
unsigned short data type.That is why raw data range(0-4095) is shifted to
unsigned short range (0-65536) what I guess.
When I checked data range when read by vtkdicomimagereader,it is short data
type and range is from -32768 to +32767.

With Kind Regards,
Mallikarjun
On Feb 10, 2016 9:08 PM, "Cory Quammen" <cory.quammen at kitware.com> wrote:

> Yep, what Simon said.
>
> Cory
>
> On Wed, Feb 10, 2016 at 9:34 AM, Simon ESNEAULT <simon.esneault at gmail.com>
> wrote:
>
>> 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:
>>>>>>> http://public.kitware.com/mailman/listinfo/vtkusers
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>
>>> Search the list archives at: http://markmail.org/search/?q=vtkusers
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/vtkusers
>>>
>>>
>>
>>
>> --
>> ------------------------------------------------------------------
>> Simon Esneault
>> Rennes, France
>> ------------------------------------------------------------------
>>
>
>
>
> --
> Cory Quammen
> R&D Engineer
> Kitware, Inc.
>
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