questions > Warning: Slice timing appears corrupted Siemens Skyra
Sep 29, 2023  05:09 PM | jhs69
Warning: Slice timing appears corrupted Siemens Skyra

Hello,


 


I am trying to convert some old DICOM files to nifti, but have gotten an error warning me that my slice times may be corrupted. Upon investigation, many of the slice timings are greater than my TR. The issue does not appear to be due to incorrect units (eg TR in seconds and slice timings in milliseconds). I have provided the JSON contents below and happy to provide additional information if helpful. Any suggestions on how to approach this issue would be greatly appreciated!

JSON contents:
{
  "AcquisitionMatrixPE": 98,
  "AcquisitionNumber": 1,
  "AcquisitionTime": "09:36:53.452500",
  "BandwidthPerPixelPhaseEncode": 14.789,
  "BaseResolution": 98,
  "BodyPartExamined": "BRAIN",
  "CoilCombinationMethod": "Sum of Squares",
  "ConsistencyInfo": "N4_VD13A_LATEST_20120616",
  "ConversionSoftware": "dcm2niix",
  "ConversionSoftwareVersion": "v1.0.20220720",
  "DerivedVendorReportedEchoSpacing": 0.000689978,
  "DeviceSerialNumber": "45306",
  "DwellTime": 2.9e-06,
  "EchoTime": 0.033,
  "EchoTrainLength": 86,
  "EffectiveEchoSpacing": 0.000689978,
  "FlipAngle": 65,
  "HeudiconvVersion": "0.12.2",
  "ImageComments": "SMS_MGH_V2.1; MB=5; FOVshift=4; K_PE=3; K_RO=3; CCR=1; LeakBlockOn;",
  "ImageOrientationPatientDICOM": [1, 0, 0, 0, 1, 0],
  "ImageOrientationText": "Tra",
  "ImageType": [
    "ORIGINAL",
    "PRIMARY",
    "M",
    "ND",
    "MOSAIC"
],
  "ImagingFrequency": 123.232,
  "InPlanePhaseEncodingDirectionDICOM": "COL",
  "InstitutionAddress": 
  "InstitutionName": 
  "InstitutionalDepartmentName": 
  "MRAcquisitionType": "2D",
  "MagneticFieldStrength": 3,
  "Manufacturer": "Siemens",
  "ManufacturersModelName": "Skyra",
  "MatrixCoilMode": "SENSE",
  "Modality": "MR",
  "NonlinearGradientCorrection": false,
  "PartialFourier": 0.875,
  "PatientPosition": "HFS",
  "PercentPhaseFOV": 100,
  "PercentSampling": 100,
  "PhaseEncodingDirection": "j-",
  "PhaseEncodingSteps": 86,
  "PhaseResolution": 1,
  "PixelBandwidth": 1760,
  "ProcedureStepDescription": 
  "ProtocolName": "Bold_sms_StressTask_run_1",
  "PulseSequenceDetails": "%CustomerSeq%\\ep2d_bold_sms_mgh_v22",
  "ReceiveCoilActiveElements": "HEA;HEP",
  "ReceiveCoilName": "Head_32",
  "ReconMatrixPE": 98,
  "RepetitionTime": 1.25,
  "SAR": 0.401866,
  "ScanOptions": "PFP\\FS",
  "ScanningSequence": "EP",
  "SequenceName": "epfSM2d1_98",
  "SequenceVariant": "SK",
  "SeriesDescription": "Bold_sms_StressTask_run_1",
  "SeriesNumber": 3,
  "ShimSetting": [1950, 7762, -14938, 328, -99, 573, 520, 81],
  "SliceThickness": 2,
  "SliceTiming": [0, 3.1575, 0.085, 3.24, 0.1675, 3.3225, 0.25, 3.4075, 0.3325, 3.49, 0.415, 3.5725, 0.5, 3.655, 0.5825, 3.7375, 0.665, 3.8225, 0.7475, 3.905, 0.8325, 3.9875, 0.915, 4.07, 0.9975, 4.155, 1.08, 4.2375, 1.1625, 4.32, 1.2475, 4.4025, 1.33, 4.485, 1.4125, 4.57, 1.495, 4.6525, 1.58, 4.735, 1.6625, 4.8175, 1.745, 4.9025, 1.8275, 4.985, 1.9125, 5.0675, 1.995, 5.15, 2.0775, 5.2325, 2.16, 5.3175, 2.2425, 5.4, 2.3275, 5.4825, 2.41, 5.565, 2.4925, 5.65, 2.575, 5.7325, 2.66, 5.815, 2.7425, 5.8975, 2.825, 5.98, 2.9075, 6.065, 2.99, 6.1475, 3.075],
  "SoftwareVersions": "syngo MR D13",
  "SpacingBetweenSlices": 2,
  "StationName": "221L-3T",
  "TaskName": "stress1",
  "TotalReadoutTime": 0.0669278,
  "TxRefAmp": 311.453}

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TitleAuthorDate
Warning: Slice timing appears corrupted Siemens Skyra
jhs69 Sep 29, 2023
Chris Rorden Sep 29, 2023
jhs69 Oct 2, 2023