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FSL FIRST pre-calculated inputs #3045

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FSL FIRST pre-calculated inputs #3045

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@Lestropie Lestropie commented Nov 24, 2024

Work In Progress.

Final relevant changeset being extracted from #2330 to allow its closure. I have extracted the code changes relating to addition of the -first_dir option to labelsgmfirst / 5ttgen fsl / 5ttgen hsvs and applied them to dev with authorship to @nicdc. From here I will need to:

  • Resolve against various changes made to dev since edited documentation 5ttgen hsvs -white_stem #2330 was listed. This will include use of f-strings, typed command-line argument variables, ...
  • Re-arrange some code; eg. checking validity of user input before any processing commences
  • Make code more robust to user input; eg. ideally not requiring specific filename prefixes to be used
  • Add tests that manually run FIRST, then run these scripts providing those data as input
  • Replace run.command('cp ...') with shutil

NicDC added 2 commits November 24, 2024 17:27
Original commit message:
"Added option to provide FSL FIRST data to three scripts which would otherwise run that step repeatedly.
Also takes away the FSL dependency in labelsgmfix for Windows users."
Manual cherry-pick of dc6d87b by: Robert E. Smith <[email protected]>
Manual application of changes in #2330 by: Robert E. Smith <[email protected]>
@Lestropie Lestropie added this to the 3.1.0 updates milestone Nov 24, 2024
@Lestropie Lestropie self-assigned this Nov 24, 2024
@Lestropie Lestropie changed the title Fsl first precalc FSL FIRST pre-calculated inputs Nov 24, 2024
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clang-tidy review says "All clean, LGTM! 👍"

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clang-tidy review says "All clean, LGTM! 👍"

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