[Insight-users] CenteredAffineTransform and DeformableRegistration6

[Alexandra Badea]

Greetings!
After a break I decided to come back to itk registration. I have used  
DeformableRegistration6 in the past, initialized with a transformed  
obtained from AIR (Woods, 1998). It proved to be a lengthy process  
(even for just a reduced volume) and I think about ways to reduce the  
computing time.
My images are 128x128x256 pixels.

I wanted to initialize my transform (by feeding images already  
registered) with a 3D centered affine transform.
To my surprise ImageRegistration9 run fine for a 2D example but if I  
change the dimension to 3 it doesn't seem to work. The program aborts  
after giving an initial estimate for the transform.
I thought that the way to do it is modify ImageRegistration9 and just  
changed the dimension from 2 to 3 in line 123.
const    unsigned int    Dimension = 3;

[ithaka:itk1.8/alex/build] alex%  
/Users/alex/software/itk1.8/alex/build/CenteredAffine3d  
/Users/alex/voxstation/alxbrains/N18977/recon/rHippocampus.hdr  
/Users/alex/voxstation/alxbrains/N19101/recon/rHippocampus.hdr  
/Users/alex/software/itk/alex/data/reg3d.hdr
Initial Transform Parameters
[1, 0, 0, 0, 1, 0, 0, 0, 1, 5.47948, 4.84506, 11.925, -0.102522,  
0.0548602, 0.350592]
0   5.30472e+06   [1, 0, 0, 0, 1, 0, 0, 0, nan, 5.47948, 4.84506,  
11.925, -0.102522, nan, nan]


/Users/alex/software/itk1.8/InsightToolkit-1.8.0/Utilities/vxl/core/ 
vnl/vnl_matrix.txx: 1151: matrix has non-finite elements
/Users/alex/software/itk1.8/InsightToolkit-1.8.0/Utilities/vxl/core/ 
vnl/vnl_matrix.txx: here it is:
1 0 0
0 1 0
0 0 nan
/Users/alex/software/itk1.8/InsightToolkit-1.8.0/Utilities/vxl/core/ 
vnl/vnl_matrix.txx: calling abort()
Abort
[ithaka:itk1.8/alex/build] alex%


If I try to register an image to itself I get the following error:

[ithaka:itk1.8/alex/build] alex%  
/Users/alex/software/itk1.8/alex/build/CenteredAffine3d  
/Users/alex/voxstation/alxbrains/N18977/recon/rHippocampus.hdr  
/Users/alex/voxstation/alxbrains/N18977/recon/rHippocampus.hdr  
/Users/alex/software/itk/alex/data/selfreg
Initial Transform Parameters
[1, 0, 0, 0, 1, 0, 0, 0, 1, 5.47948, 4.84506, 11.925, 0, 0, 0]
0   0   [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
nan, nan, nan]


/Users/alex/software/itk1.8/InsightToolkit-1.8.0/Utilities/vxl/core/ 
vnl/vnl_matrix.txx: 1151: matrix has non-finite elements
/Users/alex/software/itk1.8/InsightToolkit-1.8.0/Utilities/vxl/core/ 
vnl/vnl_matrix.txx: here it is:
nan nan nan
nan nan nan
nan nan nan
/Users/alex/software/itk1.8/InsightToolkit-1.8.0/Utilities/vxl/core/ 
vnl/vnl_matrix.txx: calling abort()
Abort

I have the feeling that I am doing something very wrong. Can anyone  
help me identify what it is?
Also has anybody tried the DeformableRegistration6 with images of this  
size 128x128x256 and can estimate a reasonable computing time? My  
images are very simple in fact and I could use a reduced volume around  
my hippocampus, I also have two gray values only (255 for hippocampus,  
0 for the background).

Many thanks,
Alexandra

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