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Minor bugfix
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marcelzwiers committed Jan 21, 2025
1 parent 64743d5 commit 07aba23
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions bidscoin/bidscoiner.py
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
from bidscoin.utilities import unpack


def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force: bool=False, bidsmapname: str='bidsmap.yaml', cluster: str='') -> None:
def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force: bool=False, bidsmap: str= 'bidsmap.yaml', cluster: str= '') -> None:
"""
Main function that processes all the subjects and session in the sourcefolder and uses the
bidsmap.yaml file in bidsfolder/code/bidscoin to cast the data into the BIDS folder.
Expand All @@ -33,15 +33,15 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
:param bidsfolder: The name of the BIDS root folder
: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
:param force: If True, participant will be processed, regardless of existing folders in the bidsfolder. Otherwise, existing folders will be skipped
: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
: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
: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
:return: Nothing
"""

# Input checking & defaults
rawfolder = Path(sourcefolder).resolve()
bidsfolder = Path(bidsfolder).resolve()
bidsmapfile = Path(bidsmapname)
bidsmapfile = Path(bidsmap)
bidscoinfolder = bidsfolder/'code'/'bidscoin'
bidscoinfolder.mkdir(parents=True, exist_ok=True)
if not rawfolder.is_dir():
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