Fw: [Insight-users] itkRegionOfInterestImageFilter question

[Luis Ibanez]

Hi Moti,

Thanks for posting the additional details.

Could you please try calling

           UpdateLargestPosibleRegion()

instead of

           Update()

in the filter:

          VtkImageToImageFilter


from your description there seems to be a
pipeline update problem going on in your code...


Please let us know what you find after this change.


   Thanks


     Luis



-------------------
Moti Freiman wrote:
> 
> Hi Luis,
> I used ImageToVtkImageFilter and VtkImageToImageFilter which their files 
> are in the InsightApplications distribution, under the directory 
> Auxilary/vtk.
> moti
> 
>> ----- Original Message -----
>> From: "Luis Ibanez" <luis.ibanez at kitware.com>
>> To: <freiman at cs.huji.ac.il>
>> Cc: <insight-users at itk.org>
>> Sent: Wednesday, August 10, 2005 9:20 PM
>> Subject: Re: [Insight-users] itkRegionOfInterestImageFilter question
>>
>>
>>  
>>
>>> Hi Moti,
>>>
>>> How are you "copying back" the result to an itkImage object ?
>>>
>>> It may be that you are tampering with the mechanism of the
>>> pipeline update.
>>>
>>>
>>> Please let us know,
>>>
>>>
>>>    Thanks
>>>
>>>
>>>      Luis
>>>
>>>
>>>
>>> -------------------------------
>>> freiman at cs.huji.ac.il wrote:
>>>   
>>>
>>>> Hi Luis,
>>>> i just forgot to copy it to the mail, of course i used this line in the
>>>> right place.
>>>> one more comment.
>>>> right after used the filter i visualize the result using vtk, and it is
>>>>     
>>
>> as
>>  
>>
>>>> well as i want.
>>>> then i copy it back to itkImage object, and then save it, then the
>>>>     
>>
>> problem
>>  
>>
>>>> ocuures.
>>>> thanks again,
>>>> moti
>>>> Original Message:
>>>> -----------------
>>>> From: Luis Ibanez luis.ibanez at kitware.com
>>>> Date: Wed, 10 Aug 2005 11:17:15 -0400
>>>> To: freiman at cs.huji.ac.il, insight-users at itk.org
>>>> Subject: Re: [Insight-users] itkRegionOfInterestImageFilter question
>>>>
>>>>
>>>>
>>>> Hi Moti,
>>>>
>>>>
>>>> It seems that you never passed the "desiredRegion"
>>>> to the itk::RegionOfInterestImageFilter ("_filter")
>>>>
>>>>
>>>>
>>>> Please look at the usage of this filter in the ITK
>>>> Software Guide
>>>>
>>>>    http://www.itk.org/ItkSoftwareGuide.pdf
>>>>
>>>> in Section 7.6, "Extracting Region", pdf-page 298.
>>>>
>>>>
>>>>
>>>>
>>>> The source code of the example is available at
>>>>
>>>>
>>>>    Insight/Examples/IO/
>>>>      ImageReadRegionOfInterestWrite.cxx
>>>>
>>>>
>>>>
>>>> Regards,
>>>>
>>>>
>>>>    Luis
>>>>
>>>>
>>>> ----------------------------
>>>> freiman at cs.huji.ac.il wrote:
>>>>
>>>>     
>>>>
>>>>> Hello!
>>>>> I have the follwoing problem.
>>>>> i read A 3D image, then extract a region of interest and save it.
>>>>> when i try to read the extracted region again, i got a garbage image.
>>>>> below is my code:
>>>>>
>>>>> //reading part
>>>>>       VoxIo::Pointer imageio = VoxIo::New();
>>>>> imageio->SetFileDimensionality (3);
>>>>> imageio->SetDimensions (0,dim_x);
>>>>> imageio->SetDimensions (1,dim_y);
>>>>> imageio->SetDimensions (2,dim_z);
>>>>> imageio->SetByteOrderToLittleEndian();
>>>>> imageio->SetSpacing (0, spacing_x);
>>>>> imageio->SetSpacing (1, spacing_y);
>>>>> imageio->SetSpacing (2, spacing_z);
>>>>> imageio->SetOrigin (0,origin_x);
>>>>> imageio->SetOrigin (1,origin_y);
>>>>> imageio->SetOrigin (2,origin_z);
>>>>> imageio->SetHeaderSize (512);
>>>>> imageio->SetFileTypeToBinary();
>>>>>
>>>>> ReaderType::Pointer reader = ReaderType::New();
>>>>> reader->SetFileName(volumeName.c_str());
>>>>> reader->SetImageIO (imageio);
>>>>> reader->Update();
>>>>>
>>>>> //extract roi part
>>>>> ImageType::Pointer image = reader->GetOutput();
>>>>>       ImageType::IndexType start;
>>>>> start[0] = min_x;
>>>>> start[1] = min_y;
>>>>>       start[2] = min_z;
>>>>>
>>>>> ImageType::SizeType size;
>>>>> size[0] = max_x - min_x;
>>>>> size[1] = max_y - min_y;
>>>>> size[2] = max_z - min_z;
>>>>>
>>>>> ImageType::RegionType desiredRegion;
>>>>> desiredRegion.SetSize( size );
>>>>> desiredRegion.SetIndex( start );
>>>>>
>>>>> ROIFilterType::Pointer _filter = ROIFilterType::New();
>>>>>
>>>>>
>>>>> _filter->SetInput (reader->GetOutput());
>>>>>       _filter->Update();
>>>>>
>>>>>
>>>>> //writing partwhere extent hold new image extent and spacing hold 
>>>>> image
>>>>> spacing
>>>>>
>>>>>       VoxIo::Pointer imageio = VoxIo::New();
>>>>> imageio->SetFileDimensionality (3);
>>>>> imageio->SetDimensions (0,extent[1]-extent[0]);
>>>>> imageio->SetDimensions (1,extent[3]-extent[2]);
>>>>> imageio->SetDimensions (2,extent[5]-extent[4]);
>>>>> imageio->SetByteOrderToLittleEndian();
>>>>> imageio->SetSpacing (0, spacing[0]);
>>>>> imageio->SetSpacing (1, spacing[1]);
>>>>> imageio->SetSpacing (2, spacing[2]);
>>>>> imageio->SetOrigin (0,extent[0]);
>>>>> imageio->SetOrigin (1,extent[2]);
>>>>> imageio->SetOrigin (2,extent[4]);
>>>>> imageio->SetHeaderSize (512);
>>>>> imageio->SetFileTypeToBinary();
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> WriterType::Pointer writer = WriterType::New();
>>>>>
>>>>> writer->SetInput (_filter->GetOutput());
>>>>> writer->SetImageIO (imageio);
>>>>> writer->SetFileName (filename.c_str());
>>>>>       writer->Update();
>>>>> //////////////////////end/////////////////////////////////////
>>>>> then when i try to read the region i saved before i got a garbage 
>>>>> image,
>>>>> thanks.
>>>>> moti
>>>>> __
>>>>> Moti Freiman, Graduate Student.
>>>>> Medical Image Processing and Computer-Assisted Surgery Laboratory.
>>>>> School of Computer Science and Engineering.
>>>>> The Hebrew University of Jerusalem Givat Ram, Jerusalem 91904, Israel
>>>>> Phone: +(972)-2-658-5371 (laboratory)
>>>>> E-mail: freiman at cs.huji.ac.il
>>>>> WWW site: http://www.cs.huji.ac.il/~freiman
>>>>>
>>>>>
>>>>>
>>>>> --------------------------------------------------------------------
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>>>>> http://mail2web.com/ .
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Insight-users mailing list
>>>>> Insight-users at itk.org
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>>>>>
>>>>>
>>>>>       
>>>>
>>>>
>>>>
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>>>>
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>>>>     
>>>
>>>   
>>
>>
>>
>> .
>>
>>  
>>
> 
>