Hello experts,
I am new to fmriprep. Today, I successfully ran fmriprep and completed the preprocessing steps. However, I encountered a confusing issue that I would like to seek your guidance on. I collected my functional MRI data using a multiband EPI sequence. But when I reviewed the summary reports generated by fmriprep, I noticed that the functional MRI data was labeled as “Single-echo EPI sequence,” which is clearly inconsistent with the sequence I actually used.
I’m curious to know if this inconsistency could have an impact on my data. If this is due to a mistake in my settings, how can I correctly adjust the settings?
this is my code:
fmriprep $bids_root_dir $bids_root_dir/derivatives
participant
–participant-label $subj
–skip-bids-validation
–md-only-boilerplate
–fs-license-file /Users/caofeizhen/Desktop/语义与词汇组合性/fMRI_data/fmri/RawData/derivatives/license.txt
–output-spaces MNI152NLin2009cAsym:res-2
–nthreads $nthreads
–stop-on-first-crash
–mem_mb $mem_mb
–dummy-scans 6
-w $HOME
this is a func image json file:
{
"AcquisitionMatrixPE": 112,
"AcquisitionNumber": 1,
"AcquisitionTime": "08:39:17.745000",
"BandwidthPerPixelPhaseEncode": 30.788,
"BaseResolution": 112,
"BodyPartExamined": "BRAIN",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11E_LATEST_20181129",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220505",
"DerivedVendorReportedEchoSpacing": 0.000580003,
"DeviceSerialNumber": "167081",
"DwellTime": 2.2e-06,
"EchoTime": 0.03,
"EchoTrainLength": 55,
"EffectiveEchoSpacing": 0.000290002,
"FlipAngle": 90,
"HeudiconvVersion": "0.13.1",
"ImageOrientationPatientDICOM": [0.999401, 0.00451904, 0.0343046, -9.10284e-09, 0.991435, -0.130604],
"ImageOrientationText": "Tra>Cor(-7.5)>Sag(2.0)",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"NORM",
"MOSAIC"
],
"ImagingFrequency": 123.259,
"InPlanePhaseEncodingDirectionDICOM": "COL",
"InstitutionAddress": "Street StreetNo,Guangzhou,District,CN,ZIP",
"InstitutionName": "South China Normal University",
"InstitutionalDepartmentName": "Department",
"MRAcquisitionType": "2D",
"MagneticFieldStrength": 3,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"Modality": "MR",
"MultibandAccelerationFactor": 2,
"ParallelReductionFactorInPlane": 2,
"PartialFourier": 1,
"PatientPosition": "HFS",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingDirection": "j-",
"PhaseEncodingSteps": 111,
"PhaseResolution": 1,
"PixelBandwidth": 2030,
"ProcedureStepDescription": "SCNU^Wang_Suiping",
"ProtocolName": "run1",
"PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
"ReceiveCoilActiveElements": "HC1-7;NC1,2",
"ReceiveCoilName": "HeadNeck_64",
"ReconMatrixPE": 112,
"RefLinesPE": 24,
"RepetitionTime": 2,
"SAR": 0.0743318,
"ScanOptions": "FS",
"ScanningSequence": "EP",
"SequenceName": "*epfid2d1_112",
"SequenceVariant": "SK",
"SeriesDescription": "run1",
"SeriesNumber": 2,
"ShimSetting": [-1943, -7205, -8418, 459, 61, 184, -37, 36],
"SliceThickness": 2,
"SliceTiming": [0.96, 0, 1.0225, 0.065, 1.0875, 0.1275, 1.15, 0.1925, 1.215, 0.2575, 1.2775, 0.32, 1.3425, 0.385, 1.405, 0.4475, 1.47, 0.5125, 1.5325, 0.575, 1.5975, 0.64, 1.6625, 0.7025, 1.725, 0.7675, 1.79, 0.83, 1.8525, 0.895, 1.9175, 0.96, 0, 1.0225, 0.065, 1.0875, 0.1275, 1.15, 0.1925, 1.215, 0.2575, 1.2775, 0.32, 1.3425, 0.385, 1.405, 0.4475, 1.47, 0.5125, 1.5325, 0.575, 1.5975, 0.64, 1.6625, 0.7025, 1.725, 0.7675, 1.79, 0.83, 1.8525, 0.895, 1.9175],
"SoftwareVersions": "syngo MR E11",
"SpacingBetweenSlices": 2.2,
"StationName": "MRC35464",
"TaskName": "Picture",
"TotalReadoutTime": 0.0321902,
"TxRefAmp": 243.056,
"dcmmeta_affine": [
[-1.9988024234771729, -1.8205673413262957e-08, 0.07612203806638718, 109.55231475830078],
[-0.00903808418661356, 1.9828691482543945, -0.2871576249599457, -92.61264038085938],
[0.06860910356044769, 0.26120877265930176, 2.1798501014709473, -77.94599914550781],
[0.0, 0.0, 0.0, 1.0]
],
"dcmmeta_reorient_transform": [
[0.0, -1.0, 0.0, 111.0],
[1.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0],
[0.0, 0.0, 0.0, 1.0]
],
"dcmmeta_shape": [112, 112, 62, 220],
"dcmmeta_slice_dim": 2,
"dcmmeta_version": 0.6,
"global": {
"const": {
"AcquisitionMatrix": [112, 0, 0, 112],
"AngioFlag": "N",
"BitsAllocated": 16,
"BitsStored": 12,
"BodyPartExamined": "BRAIN",
"Columns": 896,
"EchoNumbers": 1,
"EchoTime": 30.0,
"EchoTrainLength": 55,
"FlipAngle": 90.0,
"HighBit": 11,
"ImageOrientationPatient": [0.99940120865366, 0.00451904207916, 0.03430455363771, -9.102837e-09, 0.9914345628851, -0.1306043931759],
"ImagePositionPatient": [-893.08285312586, -908.31346069525, 26.547248541861],
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"NORM",
"MOSAIC"
],
"ImagedNucleus": "1H",
"ImagingFrequency": 123.25914,
"InPlanePhaseEncodingDirection": "COL",
"MRAcquisitionType": "2D",
"MagneticFieldStrength": 3.0,
"Manufacturer": "SIEMENS",
"ManufacturerModelName": "Prisma_fit",
"Modality": "MR",
"NumberOfAverages": 1.0,
"NumberOfPhaseEncodingSteps": 111,
"PercentPhaseFieldOfView": 100.0,
"PercentSampling": 100.0,
"PerformedProcedureStepStartTime": "083643.980000",
"PhotometricInterpretation": "MONOCHROME2",
"PixelBandwidth": 2030.0,
"PixelRepresentation": 0,
"PixelSpacing": [2.0, 2.0],
"ProtocolName": "run1",
"RepetitionTime": 2000.0,
"Rows": 896,
"SAR": 0.07433177343653,
"SamplesPerPixel": 1,
"ScanOptions": "FS",
"ScanningSequence": "EP",
"SequenceName": "*epfid2d1_112",
"SequenceVariant": "SK",
"SeriesDescription": "run1",
"SeriesNumber": 2,
"SeriesTime": "083921.373000",
"SliceLocation": -61.35309945139,
"SliceThickness": 2.0,
"SmallestImagePixelValue": 0,
"SoftwareVersions": "syngo MR E11",
"SpacingBetweenSlices": 2.20000005131,
"SpecificCharacterSet": "ISO_IR 100",
"StudyID": "1",
"StudyTime": "083643.834000",
"TransmitCoilName": "Body",
"VariableFlipAngleFlag": "N",
"WindowCenterWidthExplanation": "Algo1"
},
"slices": {}
},
"time": {
"samples": {
"AcquisitionNumber": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220],
"AcquisitionTime": ["083917.745000", "083919.745000", "083921.745000", "083923.745000", "083925.745000", "083927.745000", "083929.745000", "083931.745000", "083933.745000", "083935.745000", "083937.745000", "083939.745000", "083941.745000", "083943.745000", "083945.745000", "083947.745000", "083949.745000", "083951.745000", "083953.745000", "083955.745000", "083957.745000", "083959.745000", "084001.745000", "084003.745000", "084005.745000", "084007.745000", "084009.745000", "084011.745000", "084013.745000", "084015.745000", "084017.745000", "084019.745000", "084021.745000", "084023.745000", "084025.745000", "084027.745000", "084029.745000", "084031.745000", "084033.745000", "084035.745000", "084037.745000", "084039.745000", "084041.745000", "084043.745000", "084045.745000", "084047.745000", "084049.745000", "084051.745000", "084053.745000", "084055.745000", "084057.745000", "084059.745000", "084101.745000", "084103.745000", "084105.745000", "084107.745000", "084109.745000", "084111.745000", "084113.745000", "084115.745000", "084117.745000", "084119.745000", "084121.745000", "084123.745000", "084125.745000", "084127.745000", "084129.745000", "084131.745000", "084133.745000", "084135.745000", "084137.745000", "084139.745000", "084141.745000", "084143.745000", "084145.745000", "084147.745000", "084149.745000", "084151.745000", "084153.745000", "084155.745000", "084157.745000", "084159.745000", "084201.745000", "084203.745000", "084205.745000", "084207.745000", "084209.745000", "084211.745000", "084213.745000", "084215.745000", "084217.745000", "084219.745000", "084221.745000", "084223.745000", "084225.745000", "084227.745000", "084229.745000", "084231.745000", "084233.745000", "084235.745000", "084237.745000", "084239.745000", "084241.745000", "084243.745000", "084245.745000", "084247.745000", "084249.745000", "084251.745000", "084253.745000", "084255.745000", "084257.745000", "084259.745000", "084301.745000", "084303.745000", "084305.745000", "084307.745000", "084309.745000", "084311.745000", "084313.745000", "084315.745000", "084317.745000", "084319.745000", "084321.745000", "084323.745000", "084325.745000", "084327.745000", "084329.745000", "084331.745000", "084333.745000", "084335.745000", "084337.745000", "084339.745000", "084341.745000", "084343.745000", "084345.745000", "084347.745000", "084349.745000", "084351.745000", "084353.745000", "084355.745000", "084357.745000", "084359.745000", "084401.745000", "084403.745000", "084405.745000", "084407.745000", "084409.745000", "084411.745000", "084413.745000", "084415.745000", "084417.745000", "084419.745000", "084421.745000", "084423.745000", "084425.745000", "084427.745000", "084429.745000", "084431.745000", "084433.745000", "084435.745000", "084437.745000", "084439.745000", "084441.745000", "084443.745000", "084445.745000", "084447.745000", "084449.745000", "084451.745000", "084453.745000", "084455.745000", "084457.745000", "084459.745000", "084501.745000", "084503.745000", "084505.745000", "084507.745000", "084509.745000", "084511.745000", "084513.745000", "084515.745000", "084517.745000", "084519.745000", "084521.745000", "084523.745000", "084525.745000", "084527.745000", "084529.745000", "084531.745000", "084533.745000", "084535.745000", "084537.745000", "084539.745000", "084541.745000", "084543.745000", "084545.745000", "084547.745000", "084549.745000", "084551.745000", "084553.745000", "084555.745000", "084557.745000", "084559.745000", "084601.745000", "084603.745000", "084605.745000", "084607.745000", "084609.745000", "084611.745000", "084613.745000", "084615.745000", "084617.745000", "084619.745000", "084621.745000", "084623.745000", "084625.745000", "084627.745000", "084629.745000", "084631.745000", "084633.745000", "084635.745000"],
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Thank you for your assistance.