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Minor bugfix
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bidscoin/bidscoiner.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@
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from bidscoin.utilities import unpack
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def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force: bool=False, bidsmapname: str='bidsmap.yaml', cluster: str='') -> None:
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def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force: bool=False, bidsmap: str= 'bidsmap.yaml', cluster: str= '') -> None:
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"""
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Main function that processes all the subjects and session in the sourcefolder and uses the
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bidsmap.yaml file in bidsfolder/code/bidscoin to cast the data into the BIDS folder.
@@ -33,15 +33,15 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
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:param bidsfolder: The name of the BIDS root folder
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:param participant: List of selected subjects/participants (i.e. sub-# names/folders) to be processed (the sub-prefix can be omitted). Otherwise, all subjects in the sourcefolder will be processed
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:param force: If True, participant will be processed, regardless of existing folders in the bidsfolder. Otherwise, existing folders will be skipped
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:param bidsmapname: The name of the bidsmap YAML-file. If the bidsmap pathname is just the basename (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin
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:param bidsmap: The name of the bidsmap YAML-file. If the bidsmap pathname is just the basename (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin
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:param cluster: Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster with DRMAA native specifications for submitting bidscoiner jobs to the HPC cluster. See cli/_bidscoiner() for default
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:return: Nothing
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"""
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# Input checking & defaults
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rawfolder = Path(sourcefolder).resolve()
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bidsfolder = Path(bidsfolder).resolve()
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bidsmapfile = Path(bidsmapname)
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bidsmapfile = Path(bidsmap)
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bidscoinfolder = bidsfolder/'code'/'bidscoin'
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bidscoinfolder.mkdir(parents=True, exist_ok=True)
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if not rawfolder.is_dir():

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