Hi,
I am not able to get fMRIprep to see my phasedif and mag images for distortion correction. I’ve scrolled through the BIDS rules and seem to be compliant. Not sure what I am missing here.
What I have tried…
- run a bids check and it’s not throwing any errors
- removing and adding an intendedfor field in the magnetic files
- adding a “readouttime” in the phsediff.json - just to see if it solved issue as above
- making sure the file names are correct and the same between phasedif and magnitude files
- removed the sub-utxxx/ from the intended field
- running with an updated version of the fMRIprep
- running without a bids_filter file
fMRIprep version 23.1.3 (having to run an old version)
Here are the fieldmap names…
Here is the json for the phasediff image
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.22341,
"Manufacturer": "Siemens",
"ManufacturersModelName": "MAGNETOM Vida",
"InstitutionName": "UT Health Austin 3T",
"InstitutionalDepartmentName": "Radiology",
"InstitutionAddress": "Trinity 1601B,Austin,Houston,US,78712",
"DeviceSerialNumber": "175689",
"StationName": "AWP175689",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo MR XA31",
"MRAcquisitionType": "2D",
"SeriesDescription": "GRE-FieldMapping - MagnusMed",
"ProtocolName": "GRE-FieldMapping - MagnusMed",
"ScanningSequence": "GR",
"SequenceVariant": "SP",
"PulseSequenceName": "*fm2d2r",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"P",
"NONE",
"PHASE"
],
"ImageTypeText": [
"ORIGINAL",
"PRIMARY",
"P",
"DIS2D"
],
"NonlinearGradientCorrection": true,
"SeriesNumber": 9,
"AcquisitionTime": "15:09:29.007500",
"AcquisitionNumber": 1,
"SliceThickness": 2,
"SpacingBetweenSlices": 2,
"EchoNumber": 2,
"EchoTime": 0.00719,
"TotalReadoutTime": 0.0939838,
"RepetitionTime": 0.779,
"MTState": false,
"FlipAngle": 60,
"EchoTime1": 0.00473,
"EchoTime2": 0.00719,
"B0FieldIdentifier": "phasediff",
"PartialFourier": 1,
"BaseResolution": 64,
"ShimSetting": [
-1781,
-1870,
9335,
269,
-353,
-149,
103,
91
],
"TxRefAmp": 322.4,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_64_CS",
"ReceiveCoilActiveElements": "HC1-7",
"CoilString": "HeadNeck_64_CS",
"PulseSequenceDetails": "%SiemensSeq%\\gre_field_mapping",
"CoilCombinationMethod": "Sum of Squares",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingSteps": 64,
"FrequencyEncodingSteps": 64,
"AcquisitionMatrixPE": 64,
"ReconMatrixPE": 64,
"AcquisitionDuration": 98.922,
"PixelBandwidth": 1056,
"DwellTime": 7.4e-06,
"PhaseEncodingDirection": "j",
"ImageOrientationPatientDICOM": [
0.999998,
0.000114196,
-0.00201576,
-6.02368e-08,
0.998401,
0.0565311
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"IntendedFor": "ses-01/func/sub-ut0010_ses-01_task-rest_dir-AP_run-01_bold.nii.gz",
"ConversionSoftwareVersion": "v1.0.20230411",
"Dcm2bidsVersion": "3.1.0"
}
No joy