Dear all,
I have been experimenting with using fMRIprep 1.5.0rc1. My BIDS-formatted data folder also contains task events files, such as ‘./sub-01/func/sub-01_task-Emotion_run-1_events.tsv’.
Strangely, when these files had a ‘run’ key in their filename, then fMRIprep 1.5.0rc1 (but not 1.4.1) exited with an error right after BIDS validation. But when I deleted the ‘run’ key (changing the file name to ‘sub-01_task-Emotion_x-1_events.tsv’), fMRIprep seemed to continue running fine.
I copied the error at the end of this message. I hope it is useful! Please let me know if you need any other information. My current workaround is simply to delete ‘*events.tsv’ files from a data set that I am running fMRIprep on. fMRIprep 1.5.0rc1 still seems very helpful though, as I seemed to have memory usage issues with 1.4.1 when I tried running it on a cluster.
Many thanks,
Andres
Research Assistant for cognitive fMRI projects at the University of Edinburgh
## Console output
STARTING 67f6c8b8-9bfb-3a13-bc70-f14fa156a1ed
executing: fmriprep
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
14 Files, 919.43MB Emotion T1w
1 - Subject T2w
1 - Session bold
events
fieldmap
If you have any questions, please post on https://neurostars.org/tags/bids.
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 524, in build_workflow
layout = BIDSLayout(str(bids_dir), validate=False)
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 212, in __init__
indexer.index_metadata()
File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 338, in index_metadata
self.session.commit()
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1027, in commit
self.transaction.commit()
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 494, in commit
self._prepare_impl()
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 473, in _prepare_impl
self.session.flush()
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2459, in flush
self._flush(objects)
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2597, in _flush
transaction.rollback(_capture_exception=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 153, in reraise
raise value
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2557, in _flush
flush_context.execute()
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute
rec.execute(self)
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute
uow,
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 213, in save_obj
) in _organize_states_for_save(base_mapper, states, uowtransaction):
File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 408, in _organize_states_for_save
% (state_str(state), instance_key, state_str(existing))
sqlalchemy.orm.exc.FlushError: New instance <Tag at 0x2b66784f7ba8> with identity key (<class 'bids.layout.models.Tag'>, ('/inp/sub-02/func/sub-02_task-Emotion_run-1_events.tsv', 'run'), None) conflicts with persistent instance <Tag at 0x2b66784c6630>
*