Summary of what happened:
Hi,
I am trying to run fmriprep version 24.0.1 and receiving the following error. I ran fmriprep version 23.2.0 on this same data and meta-data (see JSON below) without issue. Do i need to modify the JSON to run v24.0.1? If so, can anyone advise how ‘run’ should be included in the JSON to avoid this error, or point me to the BIDS documentation?
Command used (and if a helper script was used, a link to the helper script or the command generated):
unset PYTHONPATH; singularity run --cleanenv $singularity_dir/fmriprep-24.0.1.simg \
$bids_root_dir/rawdata $bids_root_dir/derivatives/preprocessed/fmriprep_v2401 \
participant \
--participant_label $subj \
--verbose \
--output-spaces MNI152NLin2009cAsym:res-native \
--fs-license-file $FS_LICENSE \
--work-dir $bids_root_dir/code/fmriprep/sub-$subj/work_v2401
Version:
24.0.1
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
240718-17:07:25,699 cli INFO:
Telemetry system to collect crashes and errors is enabled - thanks for your feedback!. Use option ``--notrack`` to opt out.
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/run.py", line 40, in main
parse_args()
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/parser.py", line 878, in parse_args
config.from_dict({})
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/config.py", line 729, in from_dict
execution.load(settings, init=initialize('execution'), ignore=ignore)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/config.py", line 240, in load
cls.init()
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/config.py", line 503, in init
cls._layout = BIDSLayout(
^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/layout.py", line 177, in __init__
_indexer(self)
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 154, in __call__
self._index_metadata()
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/bids/layout/index.py", line 487, in _index_metadata
raise BIDSConflictingValuesError(
bids.exceptions.BIDSConflictingValuesError: Conflicting values found for entity 'run' in filename /storage/group/klk37/default/R01_Marketing/bids/rawdata/sub-001/ses-1/func/sub-001_ses-1_task-foodview_run-01_bold.nii.gz (value='01') versus its JSON sidecar (value='{'Description': ''}'). Please reconcile this discrepancy.
Screenshots / relevant information:
JSON:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.252373,
"Manufacturer": "Siemens",
"ManufacturersModelName": "MAGNETOM Prisma Fit",
"InstitutionName": "Penn State SLEIC",
"InstitutionAddress": "University Park Chandlee Laboratory,State College,PA,US,16802",
"DeviceSerialNumber": "67039",
"StationName": "AWP67039",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo MR XA30",
"MRAcquisitionType": "2D",
"SeriesDescription": "foodview-1",
"ProtocolName": "foodview-1",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"PulseSequenceName": "*epfid2d1_70",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"FMRI",
"NONE"
],
"ImageTypeText": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"NORM"
],
"NonlinearGradientCorrection": false,
"SeriesNumber": 5,
"AcquisitionTime": "16:06:21.675000",
"AcquisitionNumber": 1,
"SliceThickness": 3,
"SpacingBetweenSlices": 3,
"EchoTime": 0.025,
"RepetitionTime": 2,
"MTState": false,
"FlipAngle": 90,
"PartialFourier": 1,
"BaseResolution": 70,
"ShimSetting": [
-1915,
8227,
9418,
607,
-79,
-19,
5,
11
],
"TxRefAmp": 237.646,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_20",
"ReceiveCoilActiveElements": "HE1-4",
"CoilString": "HeadNeck_20",
"PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
"CoilCombinationMethod": "Sum of Squares",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 70,
"PhaseEncodingSteps": 70,
"FrequencyEncodingSteps": 70,
"AcquisitionMatrixPE": 70,
"ReconMatrixPE": 70,
"BandwidthPerPixelPhaseEncode": 29.155,
"EffectiveEchoSpacing": 0.000489992,
"DerivedVendorReportedEchoSpacing": 0.000489992,
"AcquisitionDuration": 267.925,
"TotalReadoutTime": 0.0338094,
"PixelBandwidth": 2463,
"DwellTime": 2.9e-06,
"PhaseEncodingDirection": "j-",
"SliceTiming": [
0,
1.02,
0.0575,
1.075,
0.1125,
1.1325,
0.17,
1.1875,
0.2275,
1.245,
0.2825,
1.3025,
0.34,
1.3575,
0.3975,
1.415,
0.4525,
1.4725,
0.51,
1.5275,
0.5675,
1.585,
0.6225,
1.64,
0.68,
1.6975,
0.735,
1.755,
0.7925,
1.81,
0.85,
1.8675,
0.905,
1.925,
0.9625
],
"ImageOrientationPatientDICOM": [
0.999859,
-0.00118619,
0.016734,
4.67189e-08,
0.997497,
0.0707049
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20230411",
"Dcm2bidsVersion": "2.1.6",
"TaskName": "foodview"
}
