Hello,
we used dcm2bids to convert our MRI pilot data to BIDS (Data acquired on Siemens MAGNETOM Prisma). I upload my BIDS folder in the BIDS validator I keep getting the error below. I am afraid there might be something wrong with the export at the scanner (we choose ‘image conversion - enhanced’ and exported both in ‘create DICOM file system’ mode and with the box unchecked) . Note that I collected data two summers ago with siemens and I had no issues with the conversion.
error bids validator:
The fields ‘RepetitionTime’ and ‘AcquisitionDuration’ for this file are mutually exclusive. To specify acquisition duration, use ‘SliceTiming’ or ‘DelayTime’ (RepetitionTime - AcquisitionDuration).
- /sub-01/anat/sub-01_T1w.nii.gz
- /sub-01/fmap/sub-01_magnitude1.nii.gz
- /sub-01/fmap/sub-01_magnitude2.nii.gz
- /sub-01/fmap/sub-01_phasediff.nii.gz
- /sub-01/func/sub-01_task-WM_run-01_bold.nii.gz
- /sub-01/func/sub-01_task-WM_run-02_bold.nii.gz
- /sub-01/func/sub-01_task-WM_run-03_bold.nii.gz
When I run dcm2bids, I get no errors but the following warnings appear (even for my T1 I get a warning for incorrect slicetiming which is weird):
I am not able to attach a json file so I pasted the content below (this is for one of the functional fmri runs).
anyone with experience with this? Thank you in advance for your help!
Nina
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.241502,
"Manufacturer": "Siemens",
"ManufacturersModelName": "MAGNETOM Prisma Fit",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "Sequence Region Customer Sequences",
"SoftwareVersions": "syngo MR XA60",
"MRAcquisitionType": "2D",
"SeriesDescription": "FUNC_RUN1",
"ProtocolName": "FUNC_RUN1",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"PulseSequenceName": "*epfid2d1_104",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"FMRI",
"NONE"
],
"ImageTypeText": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"NORM"
],
"NonlinearGradientCorrection": false,
"SeriesNumber": 8,
"AcquisitionTime": "15:01:28.515000",
"AcquisitionNumber": 1,
"SliceThickness": 2,
"SpacingBetweenSlices": 2,
"EchoTime": 0.03,
"RepetitionTime": 1.5,
"MTState": false,
"FlipAngle": 65,
"PartialFourier": 1,
"BaseResolution": 104,
"ShimSetting": [
5091,
-7539,
-7718,
335,
-182,
-70,
61,
51
],
"TxRefAmp": 260.906,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_64",
"ReceiveCoilActiveElements": "HC1-7",
"CoilString": "HeadNeck_64",
"PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
"RefLinesPE": 24,
"CoilCombinationMethod": "Sum of Squares",
"MultibandAccelerationFactor": 3,
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 51,
"PhaseEncodingSteps": 104,
"FrequencyEncodingSteps": 104,
"AcquisitionMatrixPE": 104,
"ReconMatrixPE": 104,
"BandwidthPerPixelPhaseEncode": 34.341,
"ParallelReductionFactorInPlane": 2,
"ParallelAcquisitionTechnique": "SMS",
"EffectiveEchoSpacing": 0.000279997,
"DerivedVendorReportedEchoSpacing": 0.000559994,
"AcquisitionDuration": 916.417,
"TotalReadoutTime": 0.0288397,
"PixelBandwidth": 2090,
"DwellTime": 2.3e-06,
"PhaseEncodingDirection": "j",
"SliceTiming": [
1.11,
0,
0.74,
0.0625,
0.8025,
0.125,
0.865,
0.185,
0.925,
0.2475,
0.9875,
0.31,
1.05,
0.4325,
1.1725,
0.495,
1.235,
0.555,
1.295,
0.6175,
1.3575,
0.68,
1.42,
0.37,
1.11,
0,
0.74,
0.0625,
0.8025,
0.125,
0.865,
0.185,
0.925,
0.2475,
0.9875,
0.31,
1.05,
0.4325,
1.1725,
0.495,
1.235,
0.555,
1.295,
0.6175,
1.3575,
0.68,
1.42,
0.37,
1.11,
0,
0.74,
0.0625,
0.8025,
0.125,
0.865,
0.185,
0.925,
0.2475,
0.9875,
0.31,
1.05,
0.4325,
1.1725,
0.495,
1.235,
0.555,
1.295,
0.6175,
1.3575,
0.68,
1.42,
0.37
],
"ImageOrientationPatientDICOM": [
0.999455,
-0.00309175,
0.0328565,
0.00610544,
0.995738,
-0.0920225
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"BidsGuess": [
"func",
"_acq-epfid2p2m3_dir-PA_run-8_bold"
],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20240202",
"Dcm2bidsVersion": "3.2.0",
"TaskName": "WM"
}