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…e directory temporarily, but will integrate later.
Had a couple free hours today so I integrated the new code into the snakemake workflow. Dry-run with T2w works at this point, but just has a placeholder rule to generate the warps/gifti files, as I still need to translat that matlab code. I'll give this a whirl and see what happens, at the least will give me some files so I can write the warps/gifti generation code outside of matlab
new shape injection and laplace. components tested, and workflow dry run, but running a full end to end test now.. TODO: - finish reorganizing some files (e.g. warps are still in autotop dir) - end-to-end test - add greedy to container
midsurf vis had to be disabled for now, since without extrapolate we have nans in the surf vertices, and so nilearn plotting fails
- adds new labels for PD sink based on dilating DG into SRLM and BG, fixes problem where GM domain for PD wqs different from other coords resulting in warp ambiguity - adds new template laplace coords, from running with 1e-8 stopping criterion, above fix, and multires init (included snakefile for this) - incorporate shape inject init of laplace and the new PD sink heuristic in main workflow, cuts run time to less than 15 min total (around a minute for AP laplace)
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This should be ready to merge now:
Some remaining things to fix in a later PR:
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@jordandekraker making this draft PR so I can bring it up to date with master, and translate the warps/gifti code too. I've integrated everything else so far and tested only with dry run, will try running for real soon..