Hello,
I am using fMRIprep singularity image on HPC.
It was running just fine before, but it stopped working after installing R and AFNI on HPC. (I am just guessing it has to do with installing them cause it was working before 
)
I am getting the error below.
I tried running with different datasets, and it was the same.
Does anyone have any idea?
Thank you.
Suzzie
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/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the config_filename, ignore, force_index, and index_metadata arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the indexer argument.
warnings.warn("The ability to pass arguments to BIDSLayout that control "
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py”, line 280, in _index_metadata
payload = json.load(handle)
File “/usr/local/miniconda/lib/python3.7/json/init.py”, line 296, in load
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
File “/usr/local/miniconda/lib/python3.7/json/init.py”, line 348, in loads
return _default_decoder.decode(s)
File “/usr/local/miniconda/lib/python3.7/json/decoder.py”, line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File “/usr/local/miniconda/lib/python3.7/json/decoder.py”, line 355, in raw_decode
raise JSONDecodeError(“Expecting value”, s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 2 (char 1)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 17, in main
parse_args()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py”, line 592, in parse_args
config.from_dict(vars(opts))
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py”, line 612, in from_dict
execution.load(settings)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py”, line 218, in load
cls.init()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py”, line 448, in init
re.compile(r"^."),
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py”, line 155, in init
indexer(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py”, line 111, in call
self._index_metadata()
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py”, line 284, in _index_metadata
raise IOError(msg) from e
OSError: Error occurred while trying to decode JSON from file ‘/home/orkdir/BIDS_tutorial/fmriprep_wf/single_subject_01_wf/func_preproc_task_bart_run_01_wf/bold_confounds_wf/acc_masks/_0x65a9610e76f6bf056d6d6ae849e9f08d.json’.
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