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ds002995-mriqc: "Conflicting values found for entity 'run' in filename" #43

Open jbwexler opened 1 year ago

jbwexler commented 1 year ago

Interesting that mriqc produces this error and yet it passes the validator. Should the validator be warning about this?

Node: mriqc_wf.funcMRIQC.ComputeIQMs.metadata Working directory: /scratch1/03201/jbwexler/work_dir/mriqc/ds002995_sub-007/mriqc_wf/funcMRIQC/ComputeIQMs/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002995-mriqc..sourcedata..raw..sub-007..ses-01..func..sub-007_ses-01_task-tastemap_run-01_bold.nii.gz/metadata

Node inputs:

bids_dir = None bids_validate = True in_file = /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/mriqc/ds002995-mriqc/sourcedata/raw/sub-007/ses-01/func/sub-007_ses-01_task-tastemap_run-01_bold.nii.gz

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 576, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command raise NodeExecutionError( nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node metadata.

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/bids.py", line 807, in _run_interface self.layout = _init_layout( File "/opt/conda/lib/python3.9/site-packages/niworkflows/utils/bids.py", line 293, in _init_layout layout = BIDSLayout(str(bids_dir), validate=validate) File "/opt/conda/lib/python3.9/site-packages/bids/layout/layout.py", line 152, in init indexer(self) File "/opt/conda/lib/python3.9/site-packages/bids/layout/index.py", line 111, in call self._index_metadata() File "/opt/conda/lib/python3.9/site-packages/bids/layout/index.py", line 438, in _index_metadata raise BIDSConflictingValuesError( bids.exceptions.BIDSConflictingValuesError: Conflicting values found for entity 'run' in filename /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/mriqc/ds002995-mriqc/sourcedata/raw/sub-007/s es-01/func/sub-007_ses-01_task-tastemap_run-01_events.tsv (value='01') versus its JSON sidecar (value='{'LongName': 'Run', 'Description': 'Which run this timing segment corresponds to'}'). Please reconcile this discrepancy.