aces / Loris-MRI

The set of scripts that preprocess and insert MRI data into the database.
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[minc_to_bids_converter.pl] Error code 55 #980

Closed zaliqarosli closed 3 months ago

zaliqarosli commented 1 year ago
    1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR)
        ./dataset_description.json
            Evidence: .Authors should be array
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-1_bold.json
            Evidence: .EffectiveEchoSpacing should be number
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .EffectiveEchoSpacing should be number
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[1] should be >= 0
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[3] should be >= 0
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[5] should be >= 0
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[7] should be >= 0
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[9] should be >= 0
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[11] should be >= 0
        ./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json
            Evidence: .SliceTiming[13] should be >= 0
zaliqarosli commented 1 year ago

./sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-1_bold.json Evidence: .EffectiveEchoSpacing should be number

{
    "TaskName": "rest",
    "SequenceVariant": "SK ",
    "Modality": "MRI__ ",
    "SoftwareVersions": "syngo MR B17 ",
    "SliceTiming": [
        1.255,
        0,
        1.33250000002,
        0.07750000001,
        1.41250000001,
        0.1575,
        1.49000000002,
        0.23500000002,
        1.5675,
        0.3125,
        1.64750000002,
        0.39250000002,
        1.72500000001,
        0.47,
        1.80250000002,
        0.55000000002,
        1.88250000001,
        0.6275,
        1.96000000002,
        0.70500000002,
        2.04000000001,
        0.785,
        2.11750000002,
        0.86250000002,
        2.19500000001,
        0.94,
        2.27500000002,
        1.02000000002,
        2.35250000001,
        1.0975,
        2.43000000002,
        1.17500000002
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL  ",
    "SequenceName": "*epfid2d1_64 ",
    "SAR": 0.09241824984141,
    "PercentPhaseFOV": 100,
    "PulseSequenceType": "*epfid2d1_64 ",
    "ImageType": "ORIGINAL\\\\PRIMARY\\\\FMRI\\\\NONE\\\\ND\\\\MOSAIC ",
    "SliceOrder": "interleaved ",
    "ProtocolName": "Rest_IBIS  ",
    "FlipAngle": 90,
    "MagneticFieldStrength": 3,
    "RepetitionTime": 2.5,
    "ScanningSequence": "EP ",
    "PixelBandwidth": 1905,
    "PhaseEncodingSteps": 64,
    "EchoNumber": 1,
    "TotalReadoutTime": "not supplied as the values read from the MINC header seem erroneous, due most likely to a dcm2mnc conversion problem",
    "PatientPosition": "HFS  ",
    "EffectiveEchoSpacing": "not supplied as the values read from the MINC header seem erroneous, due most likely to a dcm2mnc conversion problem",
    "ImagingFrequency": 123.208496,
    "SeriesDescription": "Rest_IBIS  ",
    "Manufacturer": "SIEMENS  ",
    "ReceiveCoilName": "HeadMatrixix\\\\ ",
    "SeriesNumber": 17,
    "MRAcquisitionType": "2D ",
    "SliceThickness": 4,
    "AcquisitionNumber": 1,
    "ImageOrientationPatientDICOM": "0.99999083972899\\\\-2.22577821e-005\\\\-0.0042801825544\\\\-4.3724682e-009\\\\0.99998647394974\\\\-0.005201145793  ",
    "ManufacturerModelName": "TrioTim  ",
    "DeviceSerialNumber": "35182  ",
    "EchoTime": 0.027
}
zaliqarosli commented 1 year ago

sub-300125/ses-V1/func/sub-300125_ses-V1_task-rest_run-2_bold.json Evidence: .SliceTiming[1] should be >= 0

{
   "PixelBandwidth" : 1905,
   "PhaseEncodingSteps" : 64,
   "EchoNumber" : 1,
   "TotalReadoutTime" : "not supplied as the values read from the MINC header seem erroneous, due most likely to a dcm2mnc conversion problem",
   "PatientPosition" : "HFS  ",
   "EffectiveEchoSpacing" : "not supplied as the values read from the MINC header seem erroneous, due most likely to a dcm2mnc conversion problem",
   "ImagingFrequency" : 123.208496,
   "SeriesDescription" : "bas_MoCoSeries ",
   "Manufacturer" : "SIEMENS  ",
   "ReceiveCoilName" : "HeadMatrixix\\\\ ",
   "SeriesNumber" : 18,
   "MRAcquisitionType" : "2D ",
   "SliceThickness" : 4,
   "AcquisitionNumber" : 1,
   "ImageOrientationPatientDICOM" : "0.99999083972899\\\\-2.22577821e-005\\\\-0.0042801825544\\\\-4.3724682e-009\\\\0.99998647394974\\\\-0.005201145793  ",
   "ManufacturerModelName" : "TrioTim  ",
   "EchoTime" : 0.027,
   "DeviceSerialNumber" : "35182  ",
   "TaskName" : "rest",
   "Modality" : "MRI__ ",
   "SequenceVariant" : "SK ",
   "SoftwareVersions" : "syngo MR B17 "
   "SliceTiming" : [
      0,
      -1.255,
      0.07750000001,
      -1.17749999999,
      0.1575,
      -1.0975,
      0.23500000002,
      -1.01999999999,
      0.3125,
      -0.9425,
      0.39250000002,
      -0.86249999999,
      0.47,
      -0.785,
      0.54750000002,
      -0.70499999999,
      0.6275,
      -0.6275,
      0.70500000002,
      -0.54999999999,
      0.785,
      -0.47,
      0.86250000002,
      -0.39249999999,
      0.94,
      -0.315,
      1.02000000002,
      -0.23499999999,
      1.0975,
      -0.1575,
      1.17500000002,
      -0.07999999999
   ],
   "InPlanePhaseEncodingDirectionDICOM" : "COL  ",
   "SequenceName" : "*epfid2d1_64 ",
   "SAR" : 0.09241824984141,
   "PercentPhaseFOV" : 100,
   "PulseSequenceType" : "*epfid2d1_64 ",
   "ProtocolName" : "Rest_IBIS  ",
   "ImageType" : "DERIVED\\\\PRIMARY\\\\FMRI\\\\ND\\\\MOCO\\\\MOSAIC  ",
   "SliceOrder" : "interleaved ",
   "FlipAngle" : 90,
   "MagneticFieldStrength" : 3,
   "RepetitionTime" : 2.5,
   "ScanningSequence" : "EP "
}
cmadjar commented 3 months ago

After having looked at it in details with Camille, those errors are due to the quality of the RB data so closing the issue as the script works well.