Summary of what happened:
I have been trying to run fmriprep on my BIDS dataset, which works successfully except for SDC. I’ve read through some of the other threads on here and tried some of the suggested fixes but it’s still not working for me.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run \
--cleanenv \
-B $bidsdir \
-B $fmriprep_tmp \
-B $cache \
-B $fmriprep_output \
-B /autofs/space/kaonashi_001/users/kylie/code/license.txt
$fmriprep \
--participant_label "$SUBJ" -\
w $fmriprep_tmp \
--output-spaces MNI152NLin2009cAsym T1w \
--ignore slicetiming \
--fs-license-file=/autofs/space/kaonashi_001/users/kylie/code/license.txt \
$bidsdir \
$fmriprep_output \
participant \
--skip-bids-validation
Version:
fmriprep-23.2.3.simg
Environment (Docker, Singularity / Apptainer, custom installation):
I am running using singularity.
Data formatted according to a validatable standard? Please provide the output of the validator:
Data format:
BIDS/
├── dataset_description.json
├── sub-HC001/
│ ├── ses-highactive/
│ │ ├── anat/
│ │ ├── fmap/
│ │ ├── func/
│ │ └── misc/
│ ├── ses-highsham/
│ │ ├── anat/
│ │ ├── fmap/
│ │ ├── func/
│ │ └── misc/
│ └── ses-lowsham/
│ ├── anat/
│ ├── fmap/
│ ├── func/
│ └── misc/
├── sub-HC002/
│ ├── ses-highactive/
│ │ ├── anat/
│ │ ├── fmap/
│ │ ├── func/
│ │ └── misc/
│ ├── ses-highsham/
│ │ ├── anat/
│ │ ├── fmap/
│ │ ├── func/
│ │ └── misc/
│ └── ses-lowsham/
│ ├── anat/
│ ├── fmap/
│ ├── func/
│ └── misc/
├── sub-HC003/
│ ├── ses-highactive/
│ │ ├── anat/
│ │ ├── fmap/
│ │ ├── func/
│ │ └── misc/
│ ├── ses-highsham/
│ │ ├── anat/
│ │ ├── fmap/
│ │ ├── func/
│ │ └── misc/
│ └── ses-lowsham/
etc.
The validator is only giving the error that misc/ is not BIDS compliant (it has other types of scans inside).
Relevant log outputs (up to 20 lines):
I don’t get any clear error messages, it runs correctly but does no SDC.
Screenshots / relevant information:
This is an example of my AP/PA json files:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.253649,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Skyra",
"InstitutionName": "Martinos Center Bay 1",
"InstitutionalDepartmentName": "Department",
"InstitutionAddress": "13th 149,Charlestown,MA,US,02129",
"DeviceSerialNumber": "45407",
"StationName": "BAY1OC",
"BodyPart": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "NAPADOW^Vitaly",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "2D",
"StudyDescription": "NAPADOW^Vitaly",
"SeriesDescription": "topup_ap",
"ProtocolName": "topup_ap",
"ScanningSequence": "EP",
"SequenceVariant": "SK\\SP",
"ScanOptions": "FS",
"SequenceName": "epse2d1_98",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"MAGNITUDE"
],
"NonlinearGradientCorrection": false,
"SeriesNumber": 8,
"AcquisitionTime": "09:17:56.230000",
"AcquisitionNumber": 1,
"SliceThickness": 2,
"SpacingBetweenSlices": 2,
"SAR": 0.172367,
"TablePosition": [
0,
0,
0
],
"EchoTime": 0.073,
"RepetitionTime": 9.17,
"SpoilingState": true,
"FlipAngle": 90,
"PartialFourier": 1,
"BaseResolution": 98,
"ShimSetting": [
-5070,
11845,
-11778,
583,
-787,
-386,
-105,
-23
],
"TxRefAmp": 325.63,
"PhaseResolution": 1,
"VendorReportedEchoSpacing": 0.00067,
"ReceiveCoilName": "HeadNeck_64",
"ReceiveCoilActiveElements": "HC1-7;NC1",
"PulseSequenceDetails": "%CustomerSeq%\\ep2d_se_sms_abcd",
"WipMemBlock": "0a970ef2-3288-425e-a772-314b38d7f622",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 98,
"PhaseEncodingSteps": 98,
"AcquisitionMatrixPE": 98,
"ReconMatrixPE": 98,
"BandwidthPerPixelPhaseEncode": 15.23,
"EffectiveEchoSpacing": 0.000669999,
"DerivedVendorReportedEchoSpacing": 0.000669999,
"TotalReadoutTime": 0.0649899,
"PixelBandwidth": 1820,
"DwellTime": 2.8e-06,
"PhaseEncodingDirection": "j-",
"SliceTiming": [
0,
4.64844,
0.125,
4.77344,
0.25,
4.89062,
0.36719,
5.01562,
0.49219,
5.14062,
0.61719,
5.25781,
0.73438,
5.38281,
0.85938,
5.5,
0.98438,
5.625,
1.10156,
5.75,
1.22656,
5.86719,
1.35156,
5.99219,
1.46875,
6.11719,
1.59375,
6.24219,
1.71094,
6.35938,
1.83594,
6.48438,
1.96094,
6.60938,
2.07812,
6.72656,
2.20312,
6.85156,
2.32812,
6.96875,
2.44531,
7.09375,
2.57031,
7.21875,
2.69531,
7.33594,
2.8125,
7.46094,
2.9375,
7.58594,
3.05469,
7.70312,
3.17969,
7.82812,
3.30469,
7.95312,
3.42969,
8.07031,
3.54688,
8.19531,
3.67188,
8.3125,
3.79688,
8.4375,
3.91406,
8.5625,
4.03906,
8.67969,
4.16406,
8.80469,
4.28125,
8.92969,
4.40625,
9.05469,
4.52344
],
"ImageOrientationPatientDICOM": [
0.999767,
-0.0102971,
-0.0189505,
0.00645628,
0.981261,
-0.192575
],
"ImageOrientationText": "Tra>Cor(-11.1)>Sag(-1.2)",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"BidsGuess": [
"fmap",
"_acq-epse2_dir-AP_run-8_epi"
],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20250505",
"Dcm2bidsVersion": "3.2.0",
"IntendedFor": [
"ses-highactive/func/sub-HC001_ses-highactive_task-brain1_bold.nii.gz",
"ses-highactive/func/sub-HC001_ses-highactive_task-brain3_bold.nii.gz",
"ses-highactive/func/sub-HC001_ses-highactive_task-rest_bold.nii.gz",
"ses-highactive/func/sub-HC001_ses-highactive_task-brain2_bold.nii.gz"
]
}
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.25365,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Skyra",
"InstitutionName": "Martinos Center Bay 1",
"InstitutionalDepartmentName": "Department",
"InstitutionAddress": "13th 149,Charlestown,MA,US,02129",
"DeviceSerialNumber": "45407",
"StationName": "BAY1OC",
"BodyPart": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "NAPADOW^Vitaly",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "2D",
"StudyDescription": "NAPADOW^Vitaly",
"SeriesDescription": "topup_pa",
"ProtocolName": "topup_pa",
"ScanningSequence": "EP",
"SequenceVariant": "SK\\SP",
"ScanOptions": "FS",
"SequenceName": "epse2d1_98",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"MAGNITUDE"
],
"NonlinearGradientCorrection": false,
"SeriesNumber": 9,
"AcquisitionTime": "09:18:27.615000",
"AcquisitionNumber": 1,
"SliceThickness": 2,
"SpacingBetweenSlices": 2,
"SAR": 0.172367,
"TablePosition": [
0,
0,
0
],
"EchoTime": 0.073,
"RepetitionTime": 9.17,
"SpoilingState": true,
"FlipAngle": 90,
"PartialFourier": 1,
"BaseResolution": 98,
"ShimSetting": [
-5070,
11845,
-11778,
583,
-787,
-386,
-105,
-23
],
"TxRefAmp": 325.63,
"PhaseResolution": 1,
"VendorReportedEchoSpacing": 0.00067,
"ReceiveCoilName": "HeadNeck_64",
"ReceiveCoilActiveElements": "HC1-7;NC1",
"PulseSequenceDetails": "%CustomerSeq%\\ep2d_se_sms_abcd",
"WipMemBlock": "8ab182c0-8248-47f1-a9c2-e77542506857",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 98,
"PhaseEncodingSteps": 98,
"AcquisitionMatrixPE": 98,
"ReconMatrixPE": 98,
"BandwidthPerPixelPhaseEncode": 15.23,
"EffectiveEchoSpacing": 0.000669999,
"DerivedVendorReportedEchoSpacing": 0.000669999,
"TotalReadoutTime": 0.0649899,
"PixelBandwidth": 1820,
"DwellTime": 2.8e-06,
"PhaseEncodingDirection": "j-",
"SliceTiming": [
0,
4.64062,
0.11719,
4.76562,
0.24219,
4.89062,
0.35938,
5.00781,
0.48438,
5.13281,
0.60938,
5.25781,
0.72656,
5.375,
0.85156,
5.5,
0.97656,
5.61719,
1.10156,
5.74219,
1.21875,
5.86719,
1.34375,
5.98438,
1.46875,
6.10938,
1.58594,
6.23438,
1.71094,
6.35156,
1.82812,
6.47656,
1.95312,
6.60156,
2.07812,
6.71875,
2.19531,
6.84375,
2.32031,
6.96875,
2.44531,
7.08594,
2.5625,
7.21094,
2.6875,
7.33594,
2.80469,
7.45312,
2.92969,
7.57812,
3.05469,
7.70312,
3.17188,
7.82031,
3.29688,
7.94531,
3.42188,
8.0625,
3.53906,
8.1875,
3.66406,
8.3125,
3.78906,
8.42969,
3.91406,
8.55469,
4.03125,
8.67969,
4.15625,
8.79688,
4.27344,
8.92188,
4.39844,
9.04688,
4.52344
],
"ImageOrientationPatientDICOM": [
0.999767,
-0.0102971,
-0.0189505,
0.00645628,
0.981261,
-0.192575
],
"ImageOrientationText": "Tra>Cor(-11.1)>Sag(-1.2)",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"BidsGuess": [
"fmap",
"_acq-epse2_dir-AP_run-9_epi"
],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20250505",
"Dcm2bidsVersion": "3.2.0",
"IntendedFor": [
"ses-highactive/func/sub-HC001_ses-highactive_task-brain1_bold.nii.gz",
"ses-highactive/func/sub-HC001_ses-highactive_task-brain3_bold.nii.gz",
"ses-highactive/func/sub-HC001_ses-highactive_task-rest_bold.nii.gz",
"ses-highactive/func/sub-HC001_ses-highactive_task-brain2_bold.nii.gz"
]
}
I have verified that my BOLD scans match the correct naming convention for IntendedFor, I’ve made sure my dataset_description.json file has DataType set to raw. I’ve sorted through log files to try and figure out where the fieldmaps are being ignored. Any help is appreciated, thank you!
Best,
Kylie