[Insight-users] A deformable registration/segmentation question

[Andrew Ho]

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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