ENH: Couple head motion and susceptibility distortion within TOPUP#548
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mgxd wants to merge 8 commits into
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ENH: Couple head motion and susceptibility distortion within TOPUP#548mgxd wants to merge 8 commits into
mgxd wants to merge 8 commits into
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Since #279, motion estimation was decoupled and performed independently of topup. This re-enables it, with some modifications listed in the topup docs: https://fsl.fmrib.ox.ac.uk/fsl/docs/diffusion/topup/index.html An overview of the changes: - removal of slice padding - now the topup config file is selected based on the input data shape, with an emphasis on speed (divisable by 4, 2, and finally 1) https://fsl.fmrib.ox.ac.uk/fsl/docs/diffusion/topup/FAQ/index.html#do-i-have-to-have-an-even-number-of-slices-to-use-topup - volumes are capped per PE - instead of averaging across all, select a max of 3 per PE direction https://fsl.fmrib.ox.ac.uk/fsl/docs/diffusion/topup/users_guide/index.html#what-data-to-acquire-in-order-to-use-topup
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## main #548 +/- ##
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+ Coverage 84.09% 84.13% +0.03%
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Files 30 30
Lines 2880 2937 +57
Branches 383 390 +7
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+ Hits 2422 2471 +49
- Misses 382 388 +6
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Reworks
init_topup_wfto have topup handle both head motion and SD estimation concurrently.A new interface
SelectPEVolumeshas been added to reduce excessive number of inputs (like in #279), based on recommendations from the topup docs. ATM, this is set to 3 pairs, but can be further reduced if needed.Additionally, the padding hack needed to process images with an uneven # of slices was removed (again, recommended by their docs) - instead their stock configs are now present and are auto-selected based on the shape of the incoming field maps. Config file used should not have a drastic effect on the field, just the processing speed.
Given that
RobustAveragewas removed,mc_methodis no longer needed and was removed frominit_topup_wf. Hadn't seen a release yet so better to remove than deprecate.