<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hi there,</span><div style="font-family:arial,sans-serif;font-size:13px">I'm wondering if there is a suitable set of tools in ITK for my purpose:</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">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.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">There are a few approaches that I am considering, some of which I gleaned from searching the mailing list:</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">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.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">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. </div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">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: <a href="http://www.itk.org/pipermail/insight-users/2004-November/011080.html" target="_blank">http://www.itk.org/pipermail/insight-users/2004-November/011080.html</a>) -- 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</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Any suggestions and insight (sorry for that) would be much appreciated!</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">Thanks,</div><div style="font-family:arial,sans-serif;font-size:13px">andrew</div></div>