Fw: [Insight-users] itkRegionOfInterestImageFilter question

[Moti Freiman]

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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>>>>
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>>>>
>>>>
>>>>        
>>>>
>>>
>>>
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>>>
>>>
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>>>
>>>      
>>>
>>    
>>
>
>
>.
>
>  
>


-- 
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