[Insight-users] Problem with itk::ResampleImagefilter

[Daanen Vincent]

Dear Itk users,

I'm facing to a problem to use ItkImageResampler to extract slice from a  3D
image.
The goal is to extract "AXIAL", "CORONAL" or "SAGITTAL" slice from a 3D
image, whatever is its native orientation.

I succeed in extracting Axial, coronal or sagittal slice from a Axial 3D
image but I can't with a coronal 3D image.

Here's what I'm doing.

Say I have a 3D image which is coronal (or closely). Given my input image
orientation close to 
X_Img_3D = (1,0,0), Y_Img_3D = (0,0,-1), Z_Img_3D=(0,1,0), when I want to
extract a patient "axial" image, I have to set output image orientation 
to
 * X_Slice = (1,0,0) ( -> = X_Img_3D)
 * Y_Slice = (0,1,0) ( -> = Z_Img_3D)
 * Z_Slice = (0,0,1) ( -> = -Y_Img_3D)
   

// Get first "Axial"  image
start[0] = 0;		// first index on X
start[1] = 0;		// first index on Y
start[2] = 0;		// first index on Z
		
itk::Point<double,3> l_Org;
m_pImg->TransformIndexToPhysicalPoint(start, l_Org);		// m_pImg is
the input 3D image
m_pResampler->SetOutputOrigin(l_Org);

//! output image Direction
TItkInputImage::DirectionType l_InputImgDir = m_pImg->GetDirection();
TItkInputImage::DirectionType l_SliceDir;

// vector X of slice is vector X of 3D image
l_SliceDir(0,0) = l_Inputdir(0,0);
l_SliceDir(1,0) = l_Inputdir(1,0);
l_SliceDir(2,0) = l_Inputdir(2,0);

// vector Y of slice is vector Z of 3D image
l_SliceDir(0,1) = l_Inputdir(0,2);
l_SliceDir(1,1) = l_Inputdir(1,2);
l_SliceDir(2,1) = l_Inputdir(2,2);

// vector Z of slice is vector -Y of 3D image
l_SliceDir(0,2) = -l_Inputdir(0,1);
l_SliceDir(1,2) = -l_Inputdir(1,1);
l_SliceDir(2,2) = -l_Inputdir(2,1);
m_pResampler->SetOutputDirection(l_SliceDir);

// Spacing -> use minimun scale to get a isotropic slice.
const TItkInputImage::SpacingType &l_InSpacing = m_pImg->GetSpacing();
double l_IsoSpacing =
__min(l_InSpacing[0],__min(l_InSpacing[1],l_InSpacing[2]));
		
TItkOutputImage::SpacingType l_OutSpacing;
l_OutSpacing[0] = l_IsoSpacing;
l_OutSpacing[1] = l_IsoSpacing;
l_OutSpacing[2] = l_IsoSpacing;
m_pResampler->SetOutputSpacing(l_OutSpacing);

// output image size
TItkOutputImage::SizeType l_OutputImgSize = inputRegion.GetSize();
TItkInputImage::SizeType size = inputRegion.GetSize();

l_OutputImgSize[0] = size[0];						//
width of axial image  = width of native image
l_OutputImgSize[1] = size[2]*l_InSpacing[1]/l_IsoSpacing;		//
height of axial image = Depth of native image * slicethickness/pixelsize
l_OutputImgSize[2] = 1; // size along Z

m_pResampler->SetSize( l_OutputImgSize );



Doing so, I get an image with a small part of the native image :(.
I must be missing something but i can't see what;

Is there a itk::ImageResampleFileter guru who could help me ?

Thanks

 Vince


--------------------------------------------
Vincent Daanen, PhD
D&D Manager

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KOELIS
5, avenue du Grand Sablon 38700 La Tronche
www.koelis.com  -  daanen at koelis.com
Tel .+33(0) 476637588 Fax .+33(0) 476637592
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