[Insight-users] 3D deformable registration

[ping chen]

Hi Luis, 

The problem I want to solve is take out same regions
of brains with registration. we have reference brain
images and its region mask, then by MaskImageFilter,
we can get the region of reference brain, then by
using the transformation information given by
deformableRegistration1, we warp the region of the
reference image, and get the region from the subject
brain.

I have used the MaskImageFilter to get the region i
need. and then i try to use WarpImageFilter to get the
warped region. 


I have three questions. 


through deformableRegistration1, the registration of
the fixed 3d brain image and moving 3d brain images
has finished.

1. in deformableRegistration1, the transformation
information is saved by X->WriteDisplacementField,
right? since we are dealing with 3d dataset, we need
to uncomment  X->WriteDisplacementField(2); right?
 
or can we just use   
X->WriteDisplacementFieldMultiComponent();  is this
for save the whole transform information? 

2.  how to use the above saved transform information
in warpimagefilter in 
warper->SetDeformationField( ???); 

3.  warp the region image of the reference image to
subject image with the available transform
information, or warp the region mask(binary) of
reference image and then add MaskImageFilter with the
whole warped brain will produce the same results? 

-Emily


--- Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
> Hi Emily,
> 
> 
> 1) You can mask a region of an image by
>     using the AND image filter.
>  
>
http://www.itk.org/Insight/Doxygen/html/classitk_1_1AndImageFilter.html
>     This will work ok if both the mask and
>     the image are of the same pixel type and
>     are of "integer" type: {char, short, int,
>     long}.
> 
> 
> 2) You resample the moving image, using the
>     WarpImageFilter and providing the deformation
>     field.  Note that the WarpImageFilter requires
>     you to specify an Origin (in physical space)
>     and a size (in pixels) for the output image.
> 
>     What you could do is to take the region from the
>     moving image and figure out what will be its
>     bounding box once it is mapped to the coordinate
>     system of the fixed image.  Once you have such
>     bounding box, you simply feed this information
>     into the origin and size provided to the Warp
>     ImageFilter.
> 
>     The resulting image will only have the size of
>     that specified bounding box.
> 
> 
> 
> 
> Regards,
> 
> 
>     Luis
> 
> 
> ------------------
> ping chen wrote:
> 
> > Hello, 
> > 
> > I have used DeformableRegistration1.cxx to
> register 3d
> > MRI brain images and i got the warped whole brain
> > image and also the DisplacementField.  
> > 
> > I have two problems:
> > 1. If I have a mask of one region, how i can use
> this
> > mask to take out that only region from the 3d
> images?
> > 2. I wonder how i can use this transform
> information
> > from DeformableRegistration1 to warp this region,
> > instead of a whole brain?
> > 
> > Thank you.
> > emily
> > 
> > 
> > 	
> 
> 
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