[Insight-users] A deformable registration/segmentation question

[Matt McCormick]

Hi Andrew,

You may find this class useful:

  http://www.itk.org/Doxygen/html/classitk_1_1TimeVaryingVelocityFieldImageRegistrationMethodv4.html

HTH,
Matt

On Fri, Apr 26, 2013 at 7:29 PM, Andrew Ho <andrewkennethho at gmail.com> wrote:
> Hi there,
> I'm wondering if there is a suitable set of tools in ITK for my purpose:
>
> I have high-resolution 4D CT data of the human upper airway during
> swallowing. I'd like segment the upper airway and use it as the moving
> boundaries in a physics simulation. The dataset is large, but it's not too
> much to ask to manually segment it (frame by frame). The problem is that
> some interpolation is required in time. For this, it seems like a good
> approach would be to register sequential time frames and use the resulting
> deformation field to move a mesh. Then interpolation can be performed on the
> deformation field in order to advance the airway structure in time.
>
> There are a few approaches that I am considering, some of which I gleaned
> from searching the mailing list:
>
> 1) Perform 3D deformable registration between time frames (using the raw
> image data) and acquire deformation fields. Use the deformation field to
> move a mesh which is segmented from the first time frame. -- The problem
> here is that the registration problem is difficult because of the rapidly
> moving bolus (the fluid being swallowed). There is also poor contrast
> between some structures as they close the airway during the sequence.
>
> 2) Perform 3D manual segmentation on two sequential frames. Generate meshes
> from the segmented surfaces and register these two meshes. Use the resulting
> deformation field to move one mesh to the next time frame. -- The problem
> here (not really a problem) is that I don't know if a mesh to mesh
> registration (such as ICP) can be used to generate a deformable field.
>
> 3) Perform manual segmentation of the airway in frame 1 and use it as input
> to a simplex registration method on frame 2 (suggested here, way back in
> 2004: http://www.itk.org/pipermail/insight-users/2004-November/011080.html)
> -- The problem here is that I'm not sure if the segmentation will be able to
> handle the low-contrast areas when closure occurs. Another problem (again,
> not really a problem) is that the files seem to have changed and I'm not
> sure if the listed examples are still relevant
>
> Any suggestions and insight (sorry for that) would be much appreciated!
>
> Thanks,
> andrew
>
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