Add rule before Laplace-Beltrami to jointly create AP/PD src/sink boundary label masks #372
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This was referenced Feb 10, 2025
akhanf
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Feb 13, 2025
…374) - high-res ref space for hipp, dentate from shape inject (hipp default 0.3, dentate 0.1) - required adding a label wildcard to the dsegtissue and upsampled_ref files - fixes to get injected dentate/hipp working well (enough) - updated template upenn tissue dseg to include DG (only local currently) - updates to greedy registration for shape inject - downsampling for greedy template shape reg - enforce det=1 for template shape reg moments (was flipping) - dilate dentate pd src/sink (not used yet) - adjust decimation - use workaround for transforming surfaces (need to look into this bug - perhaps provide an example to HCP devs) - use two different, new, sdt threshold approaches - percentile-based for AP, and firstminima for PD - NOTE: still not perfect and should really implement #372 to make more robust
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Right now (in PR #371 ) the AP and PD boundary label masks are created independently so there is no check to ensure the same vertices are not used for both.
from the PR discussion:
JD: is there any mechanism to ensure that a vertex isn't assigned to a terminus in both AP and PD solutions? I think that ideally this would occur so that the two coords are closer to orthogonal, but maybe not strictly necessary since it would need to be done in serial rather than parallel
AK: Yes I was thinking about this too, but didn't tackle it here as the laplace beltrami rule now only as one set of src/sink. We could do this by adding a rule just upstream that takes in both AP sdt, PD sdt (and boundary mask), and outputs boundary AP/PD masks. Then laplace_beltrami could take just one pair of masks (instead of all the sdt and boundary inputs). In this script we could have also some logic to ensure the src/sink masks are also one connected component (which is not always guaranteed, especially when dist threshold very low or very high).. Could fix the labels based on some heuristic or raise an exception..
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