Summary of what happened:
Hello,
I recently updated to fmriprep version 23.1.3 to fix an issue I was having in 23.0.2. However, I’m now having issues with distortion correction with 23.1.3. Previously, the summary html files for a subject had a section “B0 Field Mapping”, but that section is completely gone from the new reports. I don’t have the IntendedFor field set in the jsons, but I do have B0FieldIdentifier and B0FieldSource so my understanding is that IntendedFor shouldn’t be needed or even used by fmriprep. I don’t notice an error anywhere, it just seems to be not recognizing the field maps, so I’m not sure how to fix it.
Thanks for your help!
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
-B ${bids_data}:/input \
-B ${bids_derivatives}:/output \
-B ${work_dir}:/work \
-B ${freesurfer_dir}:/freesurfer \
-B ${freesurfer_license}:/license.txt \
-B ${fmriprep_filter}:/fmriprep_filter.json \
${fmriprep_image} \
/input /output \
participant \
--fs-license-file /license.txt \
--skip_bids_validation \
--participant-label $sub_label \
--bids-filter-file /fmriprep_filter.json \
--work-dir /work \
--fs-subjects-dir /freesurfer \
--output-spaces fsaverage MNI152NLin6Asym fsLR func T1w fsnative \
--nprocs 16 \
--omp-nthreads 16 \
--cifti-output 91k \
--me-output-echos \
--force-bbr \
--ignore slicetiming \
--dummy-scans 10 \
--fd-spike-threshold 0.2
Version:
23.1.3
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes
Relevant log outputs (up to 20 lines):
First few lines of the log from 23.0.2:
230809-10:05:47,576 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS dataset path: /input.
* Participant list: ['002'].
* Run identifier: 20230809-094503_940b2a4f-28d6-463f-af58-3afac5dff9ba.
* Output spaces: fsaverage:den-164k MNI152NLin6Asym:res-native fsLR func T1w fsnative.
* Pre-run FreeSurfer's SUBJECTS_DIR: /output/sourcedata/freesurfer.
230809-10:06:17,972 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the following 50 estimators: [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>].
230809-10:06:18,928 nipype.workflow INFO:
No single-band-reference found for sub-002_ses-01_task-rest_run-02_echo-1_bold.nii.gz.
First few lines of the log from 23.1.3:
230809-10:44:24,825 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS dataset path: /input.
* Participant list: ['002'].
* Run identifier: 20230809-102327_51a943ea-b8a2-478d-bbd9-20f1a75cf5c6.
* Output spaces: fsaverage:den-164k MNI152NLin6Asym:res-native fsLR func T1w fsnative.
* Pre-run FreeSurfer's SUBJECTS_DIR: /freesurfer.
230809-10:44:40,747 nipype.workflow INFO:
No single-band-reference found for sub-002_ses-01_task-rest_run-02_echo-1_bold.nii.gz.
Screenshots / relevant information:
Example fmap json:
{
"AcquisitionMatrixPE": 88,
"AcquisitionNumber": 1,
"AcquisitionTime": "16:11:38.265000",
"B0FieldIdentifer": "002_01_rest02",
"BandwidthPerPixelPhaseEncode": 46.382,
"BaseResolution": 88,
"BodyPartExamined": "BRAIN",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720",
"DerivedVendorReportedEchoSpacing": 0.000490002,
"DeviceSerialNumber": "167004",
"DwellTime": 2.3e-06,
"EchoTime": 0.0286,
"EchoTrainLength": 32,
"EffectiveEchoSpacing": 0.000245001,
"FlipAngle": 70,
"ImageComments": "SENSE1",
"ImageOrientationPatientDICOM": [
0.999604,
-0.0246041,
-0.0136261,
0.0116896,
0.804098,
-0.594381
],
"ImageOrientationText": "Tra>Cor(-36.5)>Sag(-1.5)",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"MOSAIC"
],
"ImagingFrequency": 123.262,
"InPlanePhaseEncodingDirectionDICOM": "COL",
"IntendedFor": [],
"MRAcquisitionType": "2D",
"MagneticFieldStrength": 3,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"MatrixCoilMode": "GRAPPA",
"Modality": "MR",
"NonlinearGradientCorrection": true,
"ParallelReductionFactorInPlane": 2,
"PartialFourier": 0.75,
"PatientPosition": "HFS",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingDirection": "j-",
"PhaseEncodingSteps": 65,
"PhaseResolution": 1,
"PixelBandwidth": 2470,
"ProcedureStepDescription": "CRANEO^FUNCIONAL",
"ProtocolName": "RS2_AP_SE",
"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
"ReceiveCoilActiveElements": "HC1-7;NC1",
"ReceiveCoilName": "HeadNeck_64",
"ReconMatrixPE": 88,
"RefLinesPE": 24,
"RepetitionTime": 2.92,
"SAR": 0.124249,
"ScanOptions": "PFP\\FS",
"ScanningSequence": "EP",
"SequenceName": "epse2d1_88",
"SequenceVariant": "SK",
"SeriesDescription": "RS2_AP_SE",
"SeriesNumber": 18,
"ShimSetting": [
67,
-11205,
-6999,
518,
-17,
-91,
-45,
54
],
"SliceThickness": 3,
"SliceTiming": [
1.45,
0,
1.505,
0.055,
1.5625,
0.1125,
1.6175,
0.1675,
1.6725,
0.2225,
1.73,
0.28,
1.785,
0.335,
1.84,
0.39,
1.895,
0.4475,
1.9525,
0.5025,
2.0075,
0.5575,
2.0625,
0.6125,
2.12,
0.67,
2.175,
0.725,
2.23,
0.78,
2.2875,
0.8375,
2.3425,
0.8925,
2.3975,
0.9475,
2.4525,
1.005,
2.51,
1.06,
2.565,
1.115,
2.62,
1.17,
2.6775,
1.2275,
2.7325,
1.2825,
2.7875,
1.3375,
2.845,
1.395
],
"SoftwareVersions": "syngo MR E11",
"SpacingBetweenSlices": 3,
"StationName": "MRC35414",
"TotalReadoutTime": 0.010535043000000001,
"TxRefAmp": 247.336
}
Corresponding example bold json:
{
"AcquisitionMatrixPE": 88,
"AcquisitionNumber": 1,
"AcquisitionTime": "16:12:11.267500",
"B0FieldSource": "002_01_rest02",
"BandwidthPerPixelPhaseEncode": 42.882,
"BaseResolution": 88,
"BodyPartExamined": "BRAIN",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720",
"DerivedVendorReportedEchoSpacing": 0.000529996,
"DeviceSerialNumber": "167004",
"DwellTime": 2.3e-06,
"EchoNumber": 1,
"EchoTime": 0.0106,
"EchoTrainLength": 32,
"EffectiveEchoSpacing": 0.000264998,
"FlipAngle": 70,
"ImageComments": "Unaliased MB4/PE4/LB SENSE1",
"ImageOrientationPatientDICOM": [
0.999604,
-0.0246041,
-0.0136261,
0.0116896,
0.804098,
-0.594381
],
"ImageOrientationText": "Tra>Cor(-36.5)>Sag(-1.5)",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"MB",
"TE1",
"ND",
"MOSAIC"
],
"ImagingFrequency": 123.262,
"InPlanePhaseEncodingDirectionDICOM": "COL",
"MRAcquisitionType": "2D",
"MagneticFieldStrength": 3,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"MatrixCoilMode": "GRAPPA",
"Modality": "MR",
"MultibandAccelerationFactor": 4,
"NonlinearGradientCorrection": true,
"ParallelReductionFactorInPlane": 2,
"PartialFourier": 0.75,
"PatientPosition": "HFS",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingDirection": "j-",
"PhaseEncodingSteps": 65,
"PhaseResolution": 1,
"PixelBandwidth": 2470,
"ProcedureStepDescription": "CRANEO^FUNCIONAL",
"ProtocolName": "RS2",
"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold",
"ReceiveCoilActiveElements": "HC1-7;NC1",
"ReceiveCoilName": "HeadNeck_64",
"ReconMatrixPE": 88,
"RefLinesPE": 16,
"RepetitionTime": 1.5,
"SAR": 0.079801,
"ScanOptions": "PFP\\FS",
"ScanningSequence": "EP",
"SequenceName": "epfid2d5_88",
"SequenceVariant": "SK\\SS",
"SeriesDescription": "RS2",
"SeriesNumber": 21,
"ShimSetting": [
67,
-11205,
-6999,
518,
-17,
-91,
-45,
54
],
"SliceThickness": 3,
"SliceTiming": [
0,
0.7975,
0.115,
0.9125,
0.23,
1.025,
0.3425,
1.14,
0.4575,
1.2525,
0.57,
1.3675,
0.685,
0,
0.7975,
0.115,
0.9125,
0.23,
1.025,
0.3425,
1.14,
0.4575,
1.2525,
0.57,
1.3675,
0.685,
0,
0.7975,
0.115,
0.9125,
0.23,
1.025,
0.3425,
1.14,
0.4575,
1.2525,
0.57,
1.3675,
0.685,
0,
0.7975,
0.115,
0.9125,
0.23,
1.025,
0.3425,
1.14,
0.4575,
1.2525,
0.57,
1.3675,
0.685
],
"SoftwareVersions": "syngo MR E11",
"SpacingBetweenSlices": 3,
"StationName": "MRC35414",
"TaskName": "Rest",
"TotalReadoutTime": 0.011394914,
"TxRefAmp": 247.336
}