<div dir="ltr">Hi Zhang,<div><br></div><div>Please CC the vtkusers list in your replies! Also please use proper capitalization and punctuation, otherwise I will simply ignore your emails.</div><div><br></div><div>In order to average slices to reduce noise, use this vtkImageReslice method:</div><div><br></div><div> resliceFilter->SetSlabNumberOfSlices(N);</div><div><br></div><div>where N is the number of slices you want to be averaged. So, to average over 10mm when the slices have 0.4mm spacing, use N=25. The output slice spacing will still be 0.4mm.</div><div><br></div><div>The documentation for all the "Slab" methods for vtkImageReslice starts here:</div><div><a href="http://www.vtk.org/doc/nightly/html/classvtkImageReslice.html#ac46cc094b1fb577d2a3983fa2f90350d">http://www.vtk.org/doc/nightly/html/classvtkImageReslice.html#ac46cc094b1fb577d2a3983fa2f90350d</a><br></div><div><br></div><div> - David</div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 28, 2017 at 10:46 AM, <a href="mailto:zhang07101@126.com">zhang07101@126.com</a> <span dir="ltr"><<a href="mailto:zhang07101@126.com" target="_blank">zhang07101@126.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">dear david<br><br> for example, if the thickness of image is 0, the image may have lots of noise. if the.thickness of image is 10mm, the image will look more smooth. i want the thickness of resliced image to be 10mm, which will make the image more smooth. can i set the thickness for the resliced image.<br><br>zhang qiang<div class="gmail-m_-2801171349101381219quote" style="line-height:1.5"><span class="gmail-"><br><br>-------- 原始邮件 --------<br>主题：Re: [vtkusers] How to understand the slab thickness, slab resolution, spacing<br>发件人：David Gobbi <u></u><br></span>收件人：<a href="mailto:zhang07101@126.com" target="_blank">zhang07101@126.com</a>,VTK Users <u></u><br>抄送：<div><div class="gmail-h5"><br><br><br type="attribution"><blockquote class="gmail-m_-2801171349101381219quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Zhang,<div><br></div><div>Please explain exactly what you mean by "thickness". Usually only the spacing is needed for reslicing, so you need to help me understand why your situation is different.</div><div><br></div><div>Also, always CC your replies to the VTK users list.</div><div><br></div><div> - David</div><div class="gmail_extra"><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 28, 2017 at 9:19 AM, <a href="mailto:zhang07101@126.com" target="_blank">zhang07101@126.com</a> <span dir="ltr"><<a href="mailto:zhang07101@126.com" target="_blank">zhang07101@126.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear David<br><br> because i need to set the thickness in the resliced image, and vtkimagereslice can not set the thickness. vtkimageslabreslice may have function to set thickness for the resliced image. so i need to know what is the meaning of slab.<br><br>zhang qiang<div class="gmail-m_-2801171349101381219m_-3263855206804586553quote" style="line-height:1.5"><br><br>-------- 原始邮件 --------<br>主题：Re: [vtkusers] How to understand the slab thickness, slab resolution, spacing<br>发件人：David Gobbi <u></u><br>收件人：zhang qiang <u></u><br>抄送：VTK Users <u></u><br><div><div class="gmail-m_-2801171349101381219h5"><br><br type="attribution"><blockquote class="gmail-m_-2801171349101381219m_-3263855206804586553quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi Zhang,</div><div><br></div><div>To make your data isotropic, I suggest using vtkImageReslice. I don't see any reason to use vtkImageSlabReslice, but maybe you can explain in more detail why the "slab" part is important for your result.</div><div><br></div><div>VTK does not record the SliceThickness. The VTK spacing measures the distance from the center of one slice to the center of the next slice. If you need the thickness, you must get it from the DICOM metadata (e.g. you could use the vtkDICOMReader from <a href="http://github.com/dgobbi/vtk-dicom" target="_blank">github.com/dgobbi/vtk-dic<wbr>om</a>, which reads all of the metadata).</div><div><br></div><div>If you use vtkImageReslice, making the data isotropic should be as easy as this:</div><div><br></div><div><div> vtkSmartPointer<vtkImageReslic<wbr>e> resliceFilter = vtkSmartPointer<vtkImageReslic<wbr>e>::New();</div></div><div><div> resliceFilter->SetInputData(or<wbr>iginalData);</div><div> resliceFilter->SetOutputSpacin<wbr>g(0.4,0.4,0.4);</div></div><div> resliceFilter->SetInterpolatio<wbr>nModeToLinear();<br></div><div> resliceFilter->Update();</div><div><br></div><div>There is no need to call resliceFilter->SetOutputD<wbr>imensionality(3), since this is already the default.</div><div><br></div><div> - David</div><br><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 28, 2017 at 1:32 AM, zhang qiang <span dir="ltr"><<a href="mailto:zhang07101@126.com" target="_blank">zhang07101@126.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear all<br>
<br>
I feel confused about some concepts about VTK. Currently, I need to<br>
reslice a 3D data to make the data isotropic, and I use vtkImageSlabReslice.<br>
<br>
Firstly, I read the data, the code is :<br>
<br>
vtkSmartPointer<vtkDICOMImageR<wbr>eader> reader =<br>
vtkSmartPointer<vtkDICOMImageR<wbr>eader>::New();<br>
<br>
reader->SetDirectoryName("G:\\<wbr>SNAP_Signal_Analysis\\snap_sim<wbr>ulation\\SNAP_TOF_Data\\Chang<br>
Cheng\\TOF");<br>
reader->Update();<br>
<br>
vtkSmartPointer<vtkImageData> originalData = reader->GetOutput();<br>
int originalDims[3];<br>
double originalSpacing[3];<br>
originalData->GetDimensions(or<wbr>iginalDims);<br>
originalData->GetSpacing(origi<wbr>nalSpacing);<br>
<br>
My question is: how does the originalData record the data thickness<br>
information? Because I can not find the thickness from originalData.<br>
<br>
Then, I reslice the data by the following code:<br>
<br>
vtkSmartPointer<vtkImageSlabRe<wbr>slice> resliceFilter =<br>
vtkSmartPointer<vtkImageSlabRe<wbr>slice>::New();<br>
resliceFilter->SetInputData(or<wbr>iginalData);<br>
resliceFilter->SetOutputSpacin<wbr>g(0.4,0.4,0.4);<br>
//resliceFilter->SetSlabResolu<wbr>tion(0.4);<br>
resliceFilter->SetInterpolatio<wbr>nModeToLinear();<br>
resliceFilter->SetOutputDimens<wbr>ionality(3);<br>
resliceFilter->Update();<br>
<br>
Then, I check the output by:<br>
<br>
vtkSmartPointer<vtkImageData> reslicedData = resliceFilter->GetOutput();<br>
int reslicedDims[3];<br>
double reslicedSpacing[3];<br>
reslicedData->GetDimensions(re<wbr>slicedDims);<br>
reslicedData->GetSpacing(resli<wbr>cedSpacing);<br>
<br>
I find that the resliceFilter->SetSlabResoluti<wbr>on is critical to get the<br>
correct pixel spacing. Without the resliceFilter->SetSlabResoluti<wbr>on, the<br>
reslicedSpacing is (0.4,0.4,1), which means the SetOutputSpacing do not<br>
work. In the SetOutputSpacing(spacing[0],sp<wbr>aicng[1],spacing[3]), what's the<br>
meaning of spacing[3]? It is the thickness, or it is the spacing between<br>
slice?<br>
<br>
Through dicom viewer, I refer to the dicom header, and I am sure that<br>
originalSpacing[3] is the spacing between slice. So, Why<br>
resliceFilter->SetOutputSpacin<wbr>g(0.4,0.4,0.4) do not make<br>
reslicedSpacing[3]=0.4?<br>
<br>
In addition, I find two function in vtkImageSlabReslice:<br>
SetSlabThickness and SetSlabResolution. From some explanation from Internet,<br>
I guess that SetSlabThickness *NumBlendSamplePoints=SetSlabR<wbr>esolution. But,<br>
after test some case, I find it is wrong. And I have no idea about what is<br>
the relationship between slab thickness and slab resolution.<br>
<br>
zhang qiang<br></blockquote></div></div></div>
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