[vtkusers] How to understand the slab thickness, slab resolution, spacing

[David Gobbi]

Hi Zhang,

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.

Also, always CC your replies to the VTK users list.

 - David


On Fri, Jul 28, 2017 at 9:19 AM, zhang07101 at 126.com <zhang07101 at 126.com>
wrote:

> Dear David
>
> 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.
>
> zhang qiang
>
>
> -------- 原始邮件 --------
> 主题：Re: [vtkusers] How to understand the slab thickness, slab resolution,
> spacing
> 发件人：David Gobbi
> 收件人：zhang qiang
> 抄送：VTK Users
>
>
> Hi Zhang,
>
> 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.
>
> 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 github.com/dgobbi/vtk-dicom, which
> reads all of the metadata).
>
> If you use vtkImageReslice, making the data isotropic should be as easy as
> this:
>
>         vtkSmartPointer<vtkImageReslice> resliceFilter =
> vtkSmartPointer<vtkImageReslice>::New();
>         resliceFilter->SetInputData(originalData);
>         resliceFilter->SetOutputSpacing(0.4,0.4,0.4);
>         resliceFilter->SetInterpolationModeToLinear();
>         resliceFilter->Update();
>
> There is no need to call resliceFilter->SetOutputDimensionality(3), since
> this is already the default.
>
>  - David
>
>
> On Fri, Jul 28, 2017 at 1:32 AM, zhang qiang <zhang07101 at 126.com> wrote:
>
>> Dear all
>>
>>     I feel confused about some concepts about VTK. Currently, I need to
>> reslice a 3D data to make the data isotropic, and I use
>> vtkImageSlabReslice.
>>
>>     Firstly, I read the data, the code is :
>>
>> vtkSmartPointer<vtkDICOMImageReader> reader =
>> vtkSmartPointer<vtkDICOMImageReader>::New();
>>
>> reader->SetDirectoryName("G:\\SNAP_Signal_Analysis\\snap_sim
>> ulation\\SNAP_TOF_Data\\Chang
>> Cheng\\TOF");
>>         reader->Update();
>>
>>         vtkSmartPointer<vtkImageData> originalData = reader->GetOutput();
>>         int originalDims[3];
>>         double originalSpacing[3];
>>         originalData->GetDimensions(originalDims);
>>         originalData->GetSpacing(originalSpacing);
>>
>>     My question is: how does the originalData record the data thickness
>> information? Because I can not find the thickness from originalData.
>>
>>     Then, I reslice the data by the following code:
>>
>>     vtkSmartPointer<vtkImageSlabReslice> resliceFilter =
>> vtkSmartPointer<vtkImageSlabReslice>::New();
>>         resliceFilter->SetInputData(originalData);
>>         resliceFilter->SetOutputSpacing(0.4,0.4,0.4);
>>         //resliceFilter->SetSlabResolution(0.4);
>>         resliceFilter->SetInterpolationModeToLinear();
>>         resliceFilter->SetOutputDimensionality(3);
>>         resliceFilter->Update();
>>
>>     Then, I check the output by:
>>
>>     vtkSmartPointer<vtkImageData> reslicedData =
>> resliceFilter->GetOutput();
>>         int reslicedDims[3];
>>         double reslicedSpacing[3];
>>         reslicedData->GetDimensions(reslicedDims);
>>         reslicedData->GetSpacing(reslicedSpacing);
>>
>>      I find that the resliceFilter->SetSlabResolution is critical to get
>> the
>> correct pixel spacing. Without the resliceFilter->SetSlabResolution, the
>> reslicedSpacing is (0.4,0.4,1), which means the SetOutputSpacing do not
>> work. In the SetOutputSpacing(spacing[0],spaicng[1],spacing[3]), what's
>> the
>> meaning of spacing[3]? It is the thickness, or it is the spacing between
>> slice?
>>
>>      Through dicom viewer, I refer to the dicom header, and I am sure that
>> originalSpacing[3] is the spacing between slice. So, Why
>> resliceFilter->SetOutputSpacing(0.4,0.4,0.4) do not make
>> reslicedSpacing[3]=0.4?
>>
>>      In addition, I find two function in vtkImageSlabReslice:
>> SetSlabThickness and SetSlabResolution. From some explanation from
>> Internet,
>> I guess that SetSlabThickness *NumBlendSamplePoints=SetSlabResolution.
>> But,
>> after test some case, I find it is wrong. And I have no idea about what is
>> the relationship between slab thickness and slab resolution.
>>
>> zhang qiang
>>
>
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