Thank you so much for clarifying!
So essentially the TPS transform created from the landmarks is for visualization purposes only, but the landmark transfer should be assessed via the RMSE?
I definitely misunderstood this method, I thought the whole mesh deformation was part of the process to transfer the landmarks.
@agporto That’s so nice to hear that you saw my FunkyMUG talk. I switched fields now to work on clinical shoulder biomechanics but still very much interested in optimizing and automating workflows for FE model generation. I just got started with Slicer and am blown away by all of the useful plugins I have found so far.
My current goal is to transfer muscle attachment points from a muskuloskeletal model to other scapulae. Since the muscle attachment points are a bit subjective to place I plan to first use clearer anatomical landmarks to calculate the RMSE and find the best parameters for SlicerMorph, then once I identify these, I want to use them to transfer the muscle attachment points.
If it is really important for you to get a complete deformation of the mesh, it is somewhat straightforward to modify ALPACA to do it. I am happy to chat about how this can be accomplished using the machinery of the module.
Thank you very much! Do you think this could improve the accuracy of the landmark transfer? (see below).
It could also be very useful for another, more complex case I will have in the future -in our hospital CT scans, the distal humerus is missing, so ideally I would warp the generic model humerus mesh to the partial patient specific humerus (which would require whole mesh warping)
I have now tested the scapular morphing with more landmarks:
Some of the landmarks transferred quite well (the ones I placed are in green, the ones that are transferred from the source are in pink).
However, some do not transfer well:
This was with alpha and beta at .2 and CPD iterations at 1000.
Alpha and beta at 2 and CPD iterations at 1000 were a bit better (RMSE 0.007362 vs 0.008228), and closer matches, but still failing to identify certain landmarks such as the scapular notch. Note units are in meters - for reference, scapular blade height is about 15 cm).
and also showing a noticeable amount of variation near the scapular spine (an area that is important for muscle attachment points):
So I guess I should play around with increasing the alpha and beta values, and I will also test the different rigid transform options again tomorrow to see if I can get a better fit.
A quick note:
For this landmark, I think part of it is actually subjectivity in manually finding analogous points (in the source mesh, there are two angular points on the distal scapula, so there could be user disagreement where to place the point). If I had placed the source landmark here instead, that would probably give a better fit. I am just noting it here since I am sharing the files and want to note that maybe that landmark is better left out in future analyses because of lack of clarity in the manual reference landmark placement.
I also uploaded the files, they are available here:
I am not sure if I can make it to the office hours tomorrow but I will try to.
Thanks again for your help,