[Insight-users] Change orientation to 4D image

[sere f]

Hi Luis,

I would like to have the fMRI image (4D image) in Radiological convention.
could you give an help to understand where my code is wrong?

Thank you.

Serena.




On Sun, Sep 12, 2010 at 7:15 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:

>
> Hi Serena,
>
> Do you actually want to
>
> A)  resample the image ?
>
> or
>
> B)  Do you just want to change the content of the DirectionMatrix ?
>
>
> If (A), you could use the ResampleImageFilter, along with
> an AffineTransform in 4D.
>
>
> if (B), you could use the ChangeInformationImageFilter.
>
>
>
>     Regards,
>
>
>          Luis
>
>
>
> ---------------------------------------------------------------------------------
> On Thu, Sep 9, 2010 at 7:24 PM, sere f <serenaf33 at gmail.com> wrote:
>
>> Dear Users,
>>
>> I want to change the orientation of 4D image and OrientImageFilter works
>> only for 3D image.
>> I  extrapolate  3D images with ExtractImageFilter, apply the Filter
>> on OrientImageFilter and then I paste the 3D image on 4D image with
>> PasteImageFilter.
>> The final 4D image is empty and I don't understand where the error is.
>>
>> Could somebody give me a help please?
>>
>>
>> This is the code:
>>
>>
>> regionPasteM.SetIndex( Origin );
>>
>> regionPasteM.SetSize(
>> m_file1_reader->GetOutput()->GetLargestPossibleRegion().GetSize());/
>>
>> pasteimageINM->SetRegions( regionPasteM );
>>
>> pasteimageINM->Allocate();
>>
>> pasteimageINM->SetSpacing( m_file1_reader->GetOutput()->GetSpacing() );
>>
>> pasteimageINM->SetOrigin(  m_file1_reader->GetOutput()->GetOrigin());
>>
>> pasteimageINM->FillBuffer( 0 );
>>
>>   pasterM->SetInput(pasteimageINM);
>>
>> pasterM->SetSourceImage(m_file1_reader->GetOutput());
>>
>> pasterM->SetDestinationImage(pasteimageINM);
>>
>>
>>
>>  for(unsigned int i=0
>> ;i<m_file1_reader->GetOutput()->GetLargestPossibleRegion().GetSize()[3
>> ];i++)
>>
>> {
>>
>> std::cout<<"i: "<<i<<std::endl;
>>
>> InputImageType::IndexType start;
>>
>> InputImageType::SizeType size;
>>
>> start[0] =0 ;
>>
>> start[1] =0 ;
>>
>> start[2] =0 ;
>>
>> start[3] =i;
>>
>>  size[0]
>> =m_file1_reader->GetOutput()->GetLargestPossibleRegion().GetSize()[0];
>>
>> size[1]
>> =m_file1_reader->GetOutput()->GetLargestPossibleRegion().GetSize()[1];
>>
>> size[2]
>> =m_file1_reader->GetOutput()->GetLargestPossibleRegion().GetSize()[2];
>>
>> size[3] =0;
>>
>>   InputImageType::RegionType desiredRegion;
>>
>> desiredRegion.SetSize(  size  );
>>
>> desiredRegion.SetIndex( start );
>>
>> m_extractfilter->SetExtractionRegion(desiredRegion );
>>
>> m_extractfilter->SetInput(m_file1_reader->GetOutput());
>>
>>   orienter->SetInput( m_extractfilter->GetOutput() );
>>
>> orienter->SetUseImageDirection(true);
>>
>> orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::
>> ITK_COORDINATE_ORIENTATION_RPI);
>>
>> orienter->Update();
>>
>>   pasterM->SetDestinationIndex( start);
>>
>> sourceregionM.SetSize( size );
>>
>> sourceregionM.SetIndex( start);
>>
>> pasterM->SetSourceRegion(sourceregionM);
>>
>> pasterM->Update();
>>
>> pasteimageINM=pasterM->GetOutput();
>>
>>  }
>>
>>
>>
>>
>>
>>
>> Thank you very much in advance.
>>
>> Serena.
>>
>>
>>
>>
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