[FEAT] Allow for custom topup config in PEPOLAR workflow#533
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joey-scanga wants to merge 6 commits intonipreps:mainfrom
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[FEAT] Allow for custom topup config in PEPOLAR workflow#533joey-scanga wants to merge 6 commits intonipreps:mainfrom
joey-scanga wants to merge 6 commits intonipreps:mainfrom
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joey-scanga
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mgxd
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Mar 4, 2026
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Looks reasonable to me, just a few things left to address
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| if topup_config is None: | ||
| topup_config = str(data.load(f'flirtsch/b02b0{"_quick" * sloppy}.cnf')) |
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I wonder if we should add some text the workflow desc to highlight an alternative config was used
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Does cba9118 work? Should we add a copy to the fmap derivatives folder too?
Co-authored-by: Mathias Goncalves <goncalves.mathias@gmail.com>
Co-authored-by: Mathias Goncalves <goncalves.mathias@gmail.com>
Co-authored-by: Mathias Goncalves <goncalves.mathias@gmail.com>
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mgxd
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Mar 9, 2026
| if topup_config is None: | ||
| topup_config = str(data.load(f'flirtsch/b02b0{"_quick" * sloppy}.cnf')) | ||
| else: | ||
| workflow.__desc__ += f' A custom `topup` configuration file was used: {topup_config}' |
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since this could be a long filepath, i'm inclined to just say
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| workflow.__desc__ += f' A custom `topup` configuration file was used: {topup_config}' | |
| workflow.__desc__ += ' A custom `topup` configuration file was used. |
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I think I deleted these changes when trying to fork from an older version for testing purposes (2.10.0), should I just redo this off the main branch? |
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sure |
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Tested with my fork of Nibabies master (in which I'm adding a flag
--topup-config)