FSL FIRST pre-calculated inputs #3045
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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 <robert.smith@florey.edu.au>
Manual application of changes in #2330 by: Robert E. Smith <robert.smith@florey.edu.au>
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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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Noting relevance to #3073. For some (not all) MRtrix3 Python commands, it should be possible to take the outputs of third-party software commands as input rather than executing them internally. This would make it possible to utilise an MRtrix3 container that does not encapsulate those third-party softwares; the user would be responsible for generating their derivatives externally. |
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Lestropie
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fsl_first_precalc
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209636e to
67c79a8
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clang-tidy review says "All clean, LGTM! 👍" |
Conflicts: python/mrtrix3/commands/5ttgen/fsl.py python/mrtrix3/commands/5ttgen/hsvs.py python/mrtrix3/commands/labelsgmfirst.py python/mrtrix3/fsl.py
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clang-tidy review says "All clean, LGTM! 👍" |
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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_diroption tolabelsgmfirst/5ttgen fsl/5ttgen hsvsand applied them todevwith authorship to @nicdc. From here I will need to:devsince edited documentation 5ttgen hsvs -white_stem #2330 was listed. This will include use of f-strings, typed command-line argument variables, ...run.command('cp ...')withshutil