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[FIX] pybids exceptions with newer versions #174

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[FIX] pybids exceptions with newer versions #174

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23919d6
[FIX] Add flag to ignore invalid 'exclude' flag
DESm1th Nov 8, 2022
52c856d
[FIX] Remove unneeded pluralization from 'extension' flag
DESm1th Nov 8, 2022
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8 changes: 4 additions & 4 deletions ciftify/bidsapp/fmriprep_ciftify.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ def __get_bids_layout(self):
'''run the BIDS validator and produce the bids_layout'''
run("bids-validator {}".format(self.bids_dir), dryrun = DRYRUN)
try:
layout = BIDSLayout(self.bids_dir, exclude=['derivatives'])
layout = BIDSLayout(self.bids_dir, invalid_filters='allow', exclude=['derivatives'])
except:
logger.critical('Could not parse <bids_dir> {}'.format(self.bids_dir))
sys.exit(1)
Expand Down Expand Up @@ -350,7 +350,7 @@ def find_participant_bold_inputs(participant_label, settings):
suffix="bold",
session = settings.sessions if len(settings.sessions) > 0 else None,
task = settings.tasks,
extensions=["nii.gz", "nii"])
extension=["nii.gz", "nii"])

return bolds

Expand Down Expand Up @@ -381,7 +381,7 @@ def find_bold_preprocs(bold_input, settings):
space = "T1w",
suffix = 'preproc',
datatype = 'func',
extensions = ['.nii.gz', ".nii"])
extension = ['.nii.gz', ".nii"])
return bold_preprocs

#use bids derivatives layout to find the proproc files
Expand All @@ -395,7 +395,7 @@ def find_bold_preprocs(bold_input, settings):
desc = settings.preproc_desc,
suffix = "bold",
space = "T1w",
extensions=["nii.gz", "nii"])
extension=["nii.gz", "nii"])
return bold_preprocs

## now need to verify that there is only one...
Expand Down