Updates for shape injection and surf processing of injected surfaces #374
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- splits into different rules for extracting the boundary, and getting distances to src/sink masks - those new rules now produce surface maps (for easier introspection), which are passed along to the laplace beltrami rule - the dentate AP src in bbhist hemi-L was problematic with existing approach, since the PD src/sink were always closer than the AP src, so no vertices were being labelled with AP src. - in this version, we do things a little different: 1. AP and PD are done independently now 2. Instead of nearest neighbor, we use a distance threshold, which is defined based on a signed distance transform of the mask, mapped to the surface. 3. Actually there is a minimum distance, and maximum distance, along with the minimum number of vertices required in the src/sink. The threshold is swept until the desired number is reached, to deal with cases such as the above. - TODO: the get_boundary_vertices script could be further improved to perform connected components and picking the largest one, to avoid being affected by holes or other defects.. - TODO: the laplace beltrami solver doesn't take as long to run now that I am decimating alot, but if we want to further optimize things, I think the step of altering the laplacian based on the boundary conditions, after it has been made a sparse matrix, is where the inefficiency lies (based on profiling). Could try to avoid setting those weights in the first place instead of setting it after the fact.. - NOTE: solve_laplace_beltrami_open_mesh() is kept as is (except for some logging statements)
- required adding a label wildcard to the dsegtissue and upsampled_ref files - adds bbhist template and atlas files too (only locally for now)..
- updated template upenn tissue dseg to include DG (only local
currently)
- TODO add rule, used:
c3d tpl-upenn_desc-DGtissue_dseg.nii.gz -retain-labels 1 2 -as DG -binarize -popas MASK -push DG -shift 8 -push MASK -multiply tpl-upenn_desc-hipptissue_dseg.nii.gz -maximum -o tpl-upenn_desc-hippdentate_dseg.nii.gz
- downsampling for greedy template shape reg
- dilate dentate pd src/sink (not used yet)
- enforce det=1 for template shape reg moments (was flipping)
- adjust sdt dist thresholds to get upenn-injected labels working (will need to customize these based on application)
- adjust trimming for upsampled coords ref (was cutting off surf)
- adjust decimation
percentile-based for AP, and firstminima for PD
|
updated upenn dseg is uploaded to osf now, so I will merge this now to move things along.. Will see if I can try to get the updated src/sink labels and new gyrification done before I am travelling tomorrow.. |
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This PR makes changes to injection and surface processing for dealing with native surf with nnunet + injection.
files
currently)
TODO:
c3d tpl-upenn_desc-DGtissue_dseg.nii.gz -retain-labels 1 2 -as DG -binarize -popas MASK -push DG -shift 8 -push MASK -multiply tpl-upenn_desc-hipptissue_dseg.nii.gz -maximum -o tpl-upenn_desc-hippdentate_dseg.nii.gz