[Insight-users] (no subject)

Thu Aug 11 09:26:36 EDT 2005

 Hi Luis, 
 After deep investigate of my code, i found the problem. 
 it was a bug in my code, no bug in the itk part. 
 thank you very much anyway. 
 moti 

> Original Message: 
> ----------------- 
> From: Luis Ibanez luis.ibanez at kitware.com 
> Date: Wed, 10 Aug 2005 19:56:58 -0400 
> To: freiman at cs.huji.ac.il, insight-users at itk.org 
> Subject: Re: Fw: [Insight-users] itkRegionOfInterestImageFilter question 
> 
> 
> 
> 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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>>>>>> 
>>>>>>_______________________________________________ 
>>>>>>Insight-users mailing list 
>>>>>>Insight-users at itk.org 
>>>>>>http://www.itk.org/mailman/listinfo/insight-users 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>-------------------------------------------------------------------- 
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>>>>>http://mail2web.com/ . 
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>>>>> 
>>>>>_______________________________________________ 
>>>>>Insight-users mailing list 
>>>>>Insight-users at itk.org 
>>>>>http://www.itk.org/mailman/listinfo/insight-users 
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>>>. 
>>> 
>>> 
>>> 
>> 
>> 
> 
> 
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