<div dir="ltr">Your data should also be short. Once you apply the slope and intercept. Do not use unsigned short for CT data.</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 11:56 AM, Mallikarjun K <span dir="ltr"><<a href="mailto:mallikarjun49@gmail.com" target="_blank">mallikarjun49@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hello Simon and Cory,<br>
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.<br>
When I checked data range when read by vtkdicomimagereader,it is short data type and range is from -32768 to +32767.</p>
<p dir="ltr">With Kind Regards,<br>
Mallikarjun</p><div class="HOEnZb"><div class="h5">
<div class="gmail_quote">On Feb 10, 2016 9:08 PM, "Cory Quammen" <<a href="mailto:cory.quammen@kitware.com" target="_blank">cory.quammen@kitware.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Yep, what Simon said.<div><br></div><div>Cory</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 9:34 AM, Simon ESNEAULT <span dir="ltr"><<a href="mailto:simon.esneault@gmail.com" target="_blank">simon.esneault@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">Hello Mallikarjun,<br><br>If it is a CT scan, maybe you're missing the Rescale Intercept Slope parameters to get the same results as the vtkDicomImageReader ?<br><a href="https://blog.kitware.com/dicom-rescale-intercept-rescale-slope-and-itk/" target="_blank">https://blog.kitware.com/dicom-rescale-intercept-rescale-slope-and-itk/</a><br><br>Simon<br><br></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">2016-02-10 15:12 GMT+01:00 Mallikarjun K <span dir="ltr"><<a href="mailto:mallikarjun49@gmail.com" target="_blank">mallikarjun49@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Cory,<div><br></div><div>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.</div><div><br></div><div><div> //setup opacity</div><div><span style="white-space:pre-wrap"> </span>d->m_opacityTransferFunction->AddPoint(132.108911, 0.000000);</div><div><span style="white-space:pre-wrap"> </span>d->m_opacityTransferFunction->AddPoint(197.063492, 0.041333);</div><div><span style="white-space:pre-wrap"> </span>d->m_opacityTransferFunction->AddPoint(1087.917989, 0.700000);</div><div><span style="white-space:pre-wrap"> </span></div><div><span style="white-space:pre-wrap"> </span>//setup gradient opacity</div><div><span style="white-space:pre-wrap"> </span>d->m_gradientTransferFunction->AddPoint(560.695000, 1.000000);</div><div><br></div><div><span style="white-space:pre-wrap"> </span>// Setup color </div><div><span style="white-space:pre-wrap"> </span>d->m_colorTransferFunction->AddRGBPoint(176.881890, 0.650980, 0.000000, 0.000000);</div><div><span style="white-space:pre-wrap"> </span>d->m_colorTransferFunction->AddRGBPoint(239.427822, 0.933333, 0.000000, 0.000000);</div><div><span style="white-space:pre-wrap"> </span>d->m_colorTransferFunction->AddRGBPoint(301.973753, 1.000000, 0.800000, 0.062745);</div><div><span style="white-space:pre-wrap"> </span>d->m_colorTransferFunction->AddRGBPoint(495.866142, 1.000000, 0.905882, 0.666667);</div><div><span style="white-space:pre-wrap"> </span>d->m_colorTransferFunction->AddRGBPoint(677.249344, 1.000000, 0.882353, 0.215686);</div><div><span style="white-space:pre-wrap"> </span>d->m_colorTransferFunction->AddRGBPoint(808.595801, 1.000000, 1.000000, 1.000000);</div></div><div><br></div><div>What should I do to eliminate gray/balck colored stuff ? please guide me.</div><div><br></div><div>Thank you.</div><div>Regards,</div><div>Mallikarjun</div><div><br></div><div><br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 7:18 PM, Cory Quammen <span dir="ltr"><<a href="mailto:cory.quammen@kitware.com" target="_blank">cory.quammen@kitware.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">Mallikarjun,<div><br></div><div>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?</div><div><br></div><div>If it is the latter, I have a couple guesses:</div><div><br></div><div>- maybe your dimensions are off from what dcmtk tells you</div><div>- maybe dcmtk's conventions for voxel order are different from VTK<span><font color="#888888"><br></font></span></div><span><font color="#888888"><div><br></div><div>Cory</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 2:40 AM, Mallikarjun K <span dir="ltr"><<a href="mailto:mallikarjun49@gmail.com" target="_blank">mallikarjun49@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">Hello Cory Quammen,<div><br></div><div>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.</div><div><br></div><div>Below is the code snippet which I used to get dcmtk data to vtk:</div><div><br></div><div><br></div><div>vtkDataArray* scalars = 0;<br></div><div><br></div><div><br></div><div><br></div><div><div>switch (dicomDataType)</div><div><span style="white-space:pre-wrap"> </span>{</div><div><span style="white-space:pre-wrap"> </span>case TYPE_U32Data:</div><div><span style="white-space:pre-wrap"> </span>scalars = vtkUnsignedIntArray::New();</div><div><span style="white-space:pre-wrap"> </span>((vtkUnsignedIntArray*)(scalars))->SetArray((unsigned int*)dicomData, dicomDataSize, 1);//dicomData is the data from dcmtk</div><div><span style="white-space:pre-wrap"> </span>break;</div><div><span style="white-space:pre-wrap"> </span>case TYPE_U8Data:</div><div><span style="white-space:pre-wrap"> </span>scalars = vtkUnsignedCharArray::New();</div><div><span style="white-space:pre-wrap"> </span>((vtkUnsignedCharArray*)(scalars))->SetArray((unsigned char*)dicomData, dicomDataSize, 1);</div><div><span style="white-space:pre-wrap"> </span>break;</div><div><span style="white-space:pre-wrap"> </span>case TYPE_U16Data:</div><div><span style="white-space:pre-wrap"> </span>scalars = vtkUnsignedShortArray::New();</div><div><span style="white-space:pre-wrap"> </span>((vtkUnsignedShortArray*)(scalars))->SetArray((unsigned short*)dicomData, dicomDataSize, 1);</div><div><span style="white-space:pre-wrap"> </span>break;</div><div><span style="white-space:pre-wrap"> </span>case TYPE_S16Data:</div><div><span style="white-space:pre-wrap"> </span>scalars = vtkShortArray::New();</div><div><span style="white-space:pre-wrap"> </span>((vtkShortArray*)(scalars))->SetArray((short*)dicomData, dicomDataSize, 1);</div><div><span style="white-space:pre-wrap"> </span>break;</div><div><span style="white-space:pre-wrap"> </span>}</div><div><span style="white-space:pre-wrap"> </span>scalars->SetNumberOfComponents(1);</div><div><span style="white-space:pre-wrap"> </span>double range[2];</div><div><span style="white-space:pre-wrap"> </span>scalars->GetRange(range);</div><div><span style="white-space:pre-wrap"> </span>m_imageData = vtkImageData::New();</div><div><span style="white-space:pre-wrap"> </span>m_imageData->SetDimensions(dimensions);</div><div><span style="white-space:pre-wrap"> </span>m_imageData->SetSpacing(spacing);</div><div><span style="white-space:pre-wrap"> </span>m_imageData->GetPointData()->SetScalars(scalars);</div><div><span style="white-space:pre-wrap"> </span>scalars->Delete();</div><div><span style="white-space:pre-wrap"> </span>m_imageData->GetPointData()->GetScalars()->SetName("VR Cuboid");</div></div><div><br></div><div><br></div><div>Thanks&Regards,</div><div>Mallikarjun</div><div><br></div><div><br></div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">On Tue, Feb 9, 2016 at 8:47 PM, Cory Quammen <span dir="ltr"><<a href="mailto:cory.quammen@kitware.com" target="_blank">cory.quammen@kitware.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">How are you getting the data from dcmtk to VTK? Code would be helpful.<div><br></div><div>As an aside, you may be interested in David Gobbi's excellent DICOM reader for VTK.</div><div><br></div><div><a href="https://github.com/dgobbi/vtk-dicom" target="_blank">https://github.com/dgobbi/vtk-dicom</a><br></div><div><br></div><div>I believe you can build this within VTK by enabling the Module_vtkDICOM option.</div><div><br></div><div>Best,</div><div>Cory</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Tue, Feb 9, 2016 at 8:25 AM, Mallikarjun K <span dir="ltr"><<a href="mailto:mallikarjun49@gmail.com" target="_blank">mallikarjun49@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div>Hello All,</div><div>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.</div><div> <br></div><div><br></div><div><img src="cid:ii_152c619481cb9c6c" alt="Inline image 2" width="219" height="223" style="margin-right:0px"><br></div><div><br></div><div><br></div><div>When I used vtkDicomImageReader's output for Volume rendering ,I am getting the following output.</div><div><br></div><img src="cid:ii_152c618cc6879746" alt="Inline image 1" width="222" height="179"><div><br></div><div>Can anyone give some pointers why this is happening?<br clear="all"><div><br></div><div>Thanks in advance..</div><span><font color="#888888">-- <br><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><b style="font-family:tahoma,sans-serif">With Kind Regards:</b><br style="font-family:tahoma,sans-serif"><span style="font-family:tahoma,sans-serif">Mallikarjun</span></div><div dir="ltr"><font face="tahoma, sans-serif"><br></font><span style="font-family:tahoma,sans-serif"></span><div><br></div></div></div></div></div></div></div>
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