[Insight-users] ITK physical space & Image space

[Lorensen, William E (GE, Research)]

Rick,
 
If the data are read as dicom images with proper direction cosines, the itkOrientedImage can be used in place of the itkImage. itkImage does not, for efficieny reasons, take into account the directon cosines of the data.
 
Not all input formats report the direction cosines. What is you data format.
 
Bill
 
 
-----Original Message----- 
From: insight-users-bounces+lorensen=crd.ge.com at itk.org on behalf of Rick Shilling 
Sent: Thu 6/1/2006 10:46 AM 
To: insight-users at itk.org 
Cc: 
Subject: [Insight-users] ITK physical space & Image space



	Hi-
	
	I first wanted to validate a few things regarding Image to physical coordinate transformations in ITK.  All transformations are assumed to be 3-D rotation then translation.  Here's my approach:
	
	We have two scans each with different MRI scanning orientations:  sagittal & coronal.  This means that in image/pixel space,denoted as 'If' & 'Im' for image fixed & Image moving, they are not closely registered.  In fact, unit vectors are permuted & polarity is reversed in the z axis ( right handed to left handed coordinate system change).  
	
	However they have their own anatomical space (denoted as Af & Am for anatomical fixed and anatomical moving) where the two volumes are almost registered.   This means the transformation between Am to Af is close to the identity.  Note anatomical space is not physical space and I have the transformations:  If <-> Af,  Im<->Am.  
	
	I assume the transformation between image space and ITK physical space (denoted as Pf & Pm) is represented by a diagonal matrix whose diagonal entries are the anatomical pixel sizes.  This means image/Pixel directions are the same as physical directions for each volume.  Both translations are set to the zero vector.  
	
	In summary, the 6 Spaces are:
	fixed            moving
	-----------------------------
	Af                Am     |     Anatomical
	If                  Im      |     Image/Pixel
	Pf                Pm     |     ITK Physical
	
	And we have the exact transformations:
	Af   <-> If   <-> Pf
	Am <-> Im <-> Pm
	
	
	I want to give ITK the best initial estimate possible between physical spaces as a starting point to ITK registration: Pm->Pf.  Since we know in anatomical space the images are initially closely registered, we want to use that information (Am->Af=Identity) & the exact transformations as the way to compute that transformation by composing:
	Pm->Im->Am->Af->If->Pf.
	
	In our case we compute & set Pm->Pf = 
	[0 0 -1; 
	 0 1 0; 
	-1 0 0] 
	with Translation offset=
	[298;34 223];
	
	Though ITK reports:
	
	itk::ExceptionObject (00F290C8) Location: "unknown" File: C:\InsightToolkit-2.6.0\Code\Algorithms\itkMutualInformationImageToImageMetric.txx
	Line: 193 Description: itk::ERROR: MutualInformationImageToImageMetric(01262BA0): All the sampled point mapped to outside of the moving image
	
	I looked at where image/Pixel space boundaries map to in physical space for each and indeed, there is overlap.  I'm wondering if new problems are created if there is a polarity change in the physical moving to physical fixed tranformation that the programmer should know about?  Is there anything to possibly debug that you may know about?  Thanks for your help.
	
	Rick 

	
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