Summary of what happened:
the dataset: OpenNeuro
In the first run, i ran fMRIprep on the dataset as it is. In this dataset the IntendedFor field was included in the *phasediff.json but not the *magnitude*.json.
this is how the IntendedFor field looks like for the phasediff.json:
"IntendedFor": [ "func/sub-03_task-passiveview_run-1_bold.nii", "func/sub-03_task-passiveview_run-2_bold.nii", "func/sub-03_task-passiveview_run-3_bold.nii", "func/sub-03_task-passiveview_run-4_bold.nii", "func/sub-03_task-passiveview_run-5_bold.nii", "func/sub-03_task-restpost_bold.nii", "func/sub-03_task-restpre_bold.nii" ],
fMRIprep completed without any errors, on all the subjects, however none of the subject had any fmap output files; the sub-*/fmap output directories were missing
Subsequently, i’ve added the IntendedFor fields into the *magnitude*.json files and ran fMRIprep on a single subject, but just like before the fmap files/directories were missing.
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep $subdir $output participant -w $work \
--output-spaces MNI152NLin6Asym --cifti-output 91k \
--participant-label sub-$d --nthreads 16 --omp-nthreads 16 --md-only-boilerplate
Version:
25.0.0
Environment (Docker, Singularity / Apptainer, custom installation):
Manual Prepared Environment (Miniconda3-py312_25.1.1-2)
Data formatted according to a validatable standard? Please provide the output of the validator:
output frombids-validator-deno:
[WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.
AcquisitionDuration
/sub-11/func/sub-11_task-passiveview_run-1_bold.nii - Field description: Duration (in seconds) of volume acquisition.
Corresponds to DICOM Tag 0018, 9073 `Acquisition Duration`.
This field is mutually exclusive with `"RepetitionTime"`.
/sub-11/func/sub-11_task-passiveview_run-3_bold.nii - Field description: Duration (in seconds) of volume acquisition.
Corresponds to DICOM Tag 0018, 9073 `Acquisition Duration`.
This field is mutually exclusive with `"RepetitionTime"`.
336 more files with the same issue
Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.
[WARNING] TSV_ADDITIONAL_COLUMNS_UNDEFINED A TSV file has extra columns which are not defined in its associated JSON sidecar
time from script start
/sub-11/func/sub-11_task-passiveview_run-1_events.tsv
/sub-11/func/sub-11_task-passiveview_run-3_events.tsv
238 more files with the same issue
Please visit https://neurostars.org/search?q=TSV_ADDITIONAL_COLUMNS_UNDEFINED for existing conversations about this issue.
[WARNING] SUSPICIOUSLY_LONG_EVENT_DESIGN The onset of the last event is after the total duration of the corresponding scan.
This design is suspiciously long.
/sub-20/func/sub-20_task-passiveview_run-3_bold.nii
/sub-08/func/sub-08_task-passiveview_run-3_bold.nii
Please visit https://neurostars.org/search?q=SUSPICIOUSLY_LONG_EVENT_DESIGN for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
1312 Files, 137 GB passiveview MRI
49 - Subjects 1 - Sessions restpost
restpre
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
NA. no error reported.
Screenshots / relevant information:
An example of the fmap .json file
{ "Modality":"MR", "MagneticFieldStrength": 3, "ImagingFrequency": 123.254, "Manufacturer":"Siemens", "ManufacturersModelName":"Skyra", "InstitutionName":"Univie-Zahnklinik", "InstitutionalDepartmentName":"Department", "InstitutionAddress":"Sensengasse 2a,Wien,District,AT,1090", "DeviceSerialNumber":"46071", "StationName":"AWP46071", "BodyPartExamined":"BRAIN", "PatientPosition":"HFS", "ProcedureStepDescription":"FRANK^spider20", "SoftwareVersions":"syngo MR E11", "MRAcquisitionType":"2D", "SeriesDescription":"gre_field_mapping_bigFOV", "ProtocolName":"gre_field_mapping_bigFOV", "ScanningSequence":"GR", "SequenceVariant":"SP", "SequenceName":"*fm2d2r", "ImageType":[ "ORIGINAL", "PRIMARY", "P", "ND", "PHASE" ], "SeriesNumber": 14, "AcquisitionTime":"15:52:58.017500", "AcquisitionNumber": 1, "SliceThickness": 3.5, "SpacingBetweenSlices": 3.85, "SAR": 0.154313, "EchoNumber": 2, "EchoTime": 0.00738, "RepetitionTime": 0.4, "FlipAngle": 60, "EchoTime1": 0.00492, "EchoTime2": 0.00738, "PartialFourier": 1, "BaseResolution": 128, "ShimSetting":[ 8885, 10359, 4156, 752, -960, 342, 312, -46 ], "TxRefAmp": 343.703, "PhaseResolution": 1, "ReceiveCoilName":"Head_32", "ReceiveCoilActiveElements":"HEA;HEP", "PulseSequenceDetails":"%SiemensSeq%\\gre_field_mapping", "ConsistencyInfo":"N4_VE11A_LATEST_20140830", "PercentPhaseFOV": 100, "PercentSampling": 100, "PhaseEncodingSteps": 128, "AcquisitionMatrixPE": 128, "ReconMatrixPE": 128, "PixelBandwidth": 290, "DwellTime": 1.35e-05, "PhaseEncodingDirection":"i", "SliceTiming":[ 0.20312, 0, 0.21875, 0.01562, 0.23438, 0.03125, 0.23438, 0.04688, 0.25, 0.04688, 0.26562, 0.0625, 0.26562, 0.07812, 0.28125, 0.07812, 0.29688, 0.09375, 0.3125, 0.10938, 0.3125, 0.125, 0.32812, 0.125, 0.34375, 0.14062, 0.34375, 0.15625, 0.35938, 0.15625, 0.375, 0.17188, 0.375, 0.1875, 0.39062, 0.1875 ], "ImageOrientationPatientDICOM":[ 0.999673, 0.00155079, 0.0255338, -5.528e-12, 0.998161, -0.0606233 ], "InPlanePhaseEncodingDirectionDICOM":"ROW", "ConversionSoftware":"dcm2niix", "ConversionSoftwareVersion":"v1.0.20201102", "IntendedFor":[ "func/sub-03_task-restpost_bold.nii.gz", "func/sub-03_task-restpre_bold.nii.gz" ], "B0FieldIdentifier":"phasediff_fmap", "GradientSetType":"Fast", "MRTransmitCoilSequence":"Standard", "MatrixCoilMode":"SENSE", "CoilCombinationMethod":"Sum of Squares", "PulseSequenceType":"Normal", "ScanOptions":"%SiemensSeq%\\gre_field_mapping", "MTState": false, "SpoilingState": false, "NumberShots": 128, "ParallelReductionFactorInPlane": 1, "ParallelReductionFactorOutOfPlane": 1, "ParallelAcquisitionTechnique":"None", "PartialFourierDirection":"None", "EffectiveEchoSpacing": 1.35e-05, "MixingTime": 0, "TotalReadoutTime": 0.0017, "ImageOrientationText":"Tra>Cor(-1.5)>Sag(-1.4)", "SliceEncodingDirection":"k", "MultibandAccelerationFactor": 2, "InversionTime": 0.000212 }