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defacing option, upgraded dependencies

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@akhanf akhanf released this 09 Feb 15:16
· 198 commits to master since this release
  • added option for defacing (-D, disabled by default)
    • uses single T1w image (first alphanumeric match of _T1w) to deface with pydeface
    • applies it to any images in anat/ with the same FOV
    • backs-up images without defacing in sourcedata/no_defaced
    • TO DO: enable defacing of other filetypes if desired
  • added "--overwrite" option as default for heudiconv, so heuristic doesn't fail when duplicates encountered
  • Dockerfile now contains lines for setting heudiconv, bids-validator, and pydeface versions
    • currently: heudiconv=v0.5.3, validator=1.1.3, pydeface=v1.1.0
  • added flirt and fslorient Dockerfile dependencies from dropbox (without entire FSL install) for pydeface