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[ENH] Redo anatomical workflow #553

Merged
merged 25 commits into from Apr 27, 2023
Merged

[ENH] Redo anatomical workflow #553

merged 25 commits into from Apr 27, 2023

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mattcieslak
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@mattcieslak mattcieslak commented Apr 21, 2023 •
edited

The anatomical workflow was way too complex and inflexible. This PR makes some critical changes

  • Users can pick whether to use a T2w or T1w image as the anatomical reference
  • FAST and ATROPOS are replaced with SynthSeg
  • AntsBrainExtraction.sh and BET are replaced with SynthStrip
  • Nonlinear registration to the template can be skipped (so just AC-PC happens)
  • AC-PC transforms are stored in the derivatives [feature request] Save out T1/b0-to-ACPC transform to derivatives #305

In a separate PR we'll add options for supplying a template image and template brainmask (eg fmriprep outputs) as arguments.

@mattcieslak mattcieslak mentioned this pull request Apr 21, 2023
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@mattcieslak mattcieslak merged commit bde0641 into master Apr 27, 2023
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@mattcieslak mattcieslak deleted the enh/synthseg branch April 27, 2023 13:34
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