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DCAN-Labs / dcan-macaque-pipeline

The actual pipeline code, based on hcp, for non-human-primates - sp macaques.
BSD 3-Clause "New" or "Revised" License
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dev-10.5T feature additions: user-specified T1/T2 masks; ANTs T1 reg with intermediate reg to study template, 0.5 mm NMT template #6

Closed madisoth closed 3 years ago

madisoth commented 3 years ago

Adds NMT template head, brain, and mask (all resampled from 0.25 mm -> 0.5 mm)

Supports the following new options for dev-10.5T branch of nhp-abcd-bids-pipeline:

--t1-brain-mask, --t2-brain-mask: specify masks to be used in place of default masking in PreliminaryMasking + PreFreeSurfer. (Can either specify T1 mask only, or both T1 + T2).

--use-ants-reg: flag for PreFreeSurfer to do subject T1 -> atlas reg using ANTs-based script with intermediate registration to study template (AtlasRegistrationToMNI152_ANTsIntermediateTemplate_UseMasked.sh) in place of the default AtlasRegistrationToMNI152_FLIRTandFNIRT.sh

madisoth commented 3 years ago

superceded by PR #7