[vtkusers] vtkDICOMImageReader(): Anyway to change the metadata?

[sonamwangyal]

Thanks I used pydicom to get the metadata and used what you suggested and it worked!

Thank you!

Sent from my iPhone

> On Jul 13, 2017, at 4:23 PM, David Gobbi [via VTK] <ml+s1045678n5743965h66 at n5.nabble.com> wrote:
> 
> Hi Sonam,
> 
> The filter vtkImageChangeInformation can modify the spacing of the data:
> 
> ici = vtk.vtkImageChangeInformation()
> ici.SetInputConnection(reader.GetOutputPort())
> ici.SetOutputSpacing(0.859375, 0.859375, 5.0)
> 
>  - David
> 
>> On Thu, Jul 13, 2017 at 11:19 AM, Sonam Wangyal <[hidden email]> wrote:
>> Hello! 
>> 
>> This is my first post in this community and just as a heads up I am a complete newbie. I am currently working on a project to segment ventricles from MRI scans of the brain (in MATLAB). I wanted to then extract the surface using vtkDiscreteMarchingCubes() and write it into an STL file using vtkSTLWriter(). 
>> 
>> My problem is with the PixelSpacing, the documentation says if there are multiple DICOM images then the 'z' value is the Spacing Between the Slices. But I am receiving (0.859375, 0.859375, 0.0). I don't know why it is giving me a 0.0, it should be a 5. I have tried with an single DICOM and it works properly it gave me a Slice Thickness which coincidentally is the same value as the Spacing Between the Slices. 
>> 
>> SO MY QUESTION IS: is there anyway to manually change the value? My code is down below, THANKS FOR YOUR HELP! 
>> 
>> import vtk 
>> 
>> PathDicom = "./DICOMs/" 
>> reader = vtk.vtkDICOMImageReader() 
>> reader.SetDirectoryName(PathDicom) 
>> reader.Update() 
>> 
>> print(reader.GetPixelSpacing()) 
>> 
>> dmc = vtk.vtkDiscreteMarchingCubes() 
>> dmc.SetInputConnection(reader.GetOutputPort()) 
>> dmc.GenerateValues(1, 1, 1) 
>> dmc.Update() 
>> 
>> writer = vtk.vtkSTLWriter() 
>> writer.SetInputConnection(dmc.GetOutputPort()) 
>> writer.SetFileTypeToBinary() 
>> writer.SetFileName("ventricle.stl") 
>> writer.Write()
>> 
>> Cheers,
>> Sonam Wangyal
>> 
> 
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