After using heudiconv to convert dicoms to bids format, I ran fmriprep and got the following error: [ERR] “SliceTiming” value/s contains invalid value as it is greater than RepetitionTime. SliceTiming values should be in seconds not milliseconds (common mistake). (code: 66 - SLICETIMING_VALUES_GREATOR_THAN_REPETITION_TIME).
Indeed, viewing the JSON info (copied below), you can see that although the TR=2, the max slice time = 5.695. Clearly not just an issue of units (seconds vs milliseconds). FWIW, I initially ran this with an outdated version of dcm2niix but also reran with the latest version and got the same result. These data were collected on a Siemens scanner between 2019-2021.
Does anyone have suggestions as to why this error may have occurred, and more importantly, what I might do about it? Ideas I’ve seen in related threads include calculating the slice timings manually, or dividing all slice time values by a multiple (e.g., 2.8475, which would rescale the values from 0-2), but I am not confident with either approach. Happy to provide any additional info as necessary. I’ve also copied the header info from the corresponding nifti file (as output by fslhd).
{
“AcquisitionMatrixPE”: 108,
“AcquisitionNumber”: 1,
“AcquisitionTime”: “14:37:32.020000”,
“BandwidthPerPixelPhaseEncode”: 13.419,
“BaseResolution”: 108,
“CoilString”: “C:HEA;HEP”,
“ConversionSoftware”: “dcm2niix”,
“ConversionSoftwareVersion”: “v1.0.20190410 GCC6.3.0”,
“DerivedVendorReportedEchoSpacing”: 0.000690011,
“DeviceSerialNumber”: “35469”,
“DwellTime”: 2.5e-06,
“EchoTime”: 0.03,
“EffectiveEchoSpacing”: 0.000690011,
“FlipAngle”: 90,
“ImageComments”: “SMS_MGH_V2.1;_MB=3;_FOVshift=3;_K_PE=3;_K_RO=3;_CCR=1;LeakBlockOn;",
“ImageOrientationPatientDICOM”: [0.999481, -0.0146871, 0.0286756, 0.0135813, 0.999171, 0.0383838],
“ImageType”: [
“ORIGINAL”,
“PRIMARY”,
“M”,
“ND”,
“MOSAIC”
],
“ImagingFrequency”: 123.116,
“InPlanePhaseEncodingDirectionDICOM”: “COL”,
“InstitutionAddress”: “Vassar_43_Cambridge_MA_US_02139”,
“InstitutionName”: "McGovern_Institute_for_Brain_Research(3T2)”,
“InstitutionalDepartmentName”: “Department”,
“MRAcquisitionType”: “2D”,
“MagneticFieldStrength”: 3,
“Manufacturer”: “Siemens”,
“ManufacturersModelName”: “TrioTim”,
“Modality”: “MR”,
“PartialFourier”: 0.75,
“PatientPosition”: “HFS”,
“PercentPhaseFOV”: 100,
“PhaseEncodingDirection”: “j-”,
“PhaseEncodingSteps”: 81,
“PhaseResolution”: 1,
“PixelBandwidth”: 1852,
“ProcedureStepDescription”: “INVESTIGATORS_Kanwisher_Active”,
“ProtocolName”: “SMS3_2mmiso_localizer”,
“PulseSequenceDetails”: “%CustomerSeq%_ep2d_bold_sms_mgh_V21_delay”,
“ReceiveCoilName”: “32Ch_Head”,
“ReconMatrixPE”: 108,
“RepetitionTime”: 2,
“SAR”: 0.168297,
“ScanOptions”: “PFP_FS”,
“ScanningSequence”: “EP”,
“SequenceName”: “epfid2d1_108”,
“SequenceVariant”: “SK”,
“SeriesDescription”: “SMS3_2mmiso_localizer”,
“SeriesNumber”: 8,
“ShimSetting”: [6212, -28044, -24482, 345, -239, 50, -96, 188],
“SliceThickness”: 2,
“SliceTiming”: [0, 2.93, 0.0825, 3.015, 0.1675, 3.0975, 0.25, 3.1825, 0.335, 3.265, 0.4175, 3.35, 0.5025, 3.4325, 0.585, 3.5175, 0.67, 3.6, 0.7525, 3.685, 0.8375, 3.7675, 0.92, 3.8525, 1.005, 3.935, 1.0875, 4.02, 1.1725, 4.1025, 1.255, 4.1875, 1.34, 4.27, 1.4225, 4.355, 1.5075, 4.4375, 1.59, 4.5225, 1.675, 4.605, 1.7575, 4.69, 1.8425, 4.7725, 1.925, 4.8575, 2.01, 4.94, 2.0925, 5.025, 2.1775, 5.1075, 2.26, 5.1925, 2.345, 5.275, 2.4275, 5.36, 2.5125, 5.4425, 2.595, 5.5275, 2.68, 5.61, 2.7625, 5.695, 2.8475],
“SoftwareVersions”: “syngo_MR_B17”,
“SpacingBetweenSlices”: 2,
“StationName”: “MRC35469”,
“TaskName”: “EXP”,
“TotalReadoutTime”: 0.0738312,
“TxRefAmp”: 320.445}
sizeof_hdr 348
data_type INT16
dim0 4
dim1 108
dim2 108
dim3 69
dim4 209
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 2.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 2
freq_dim 1
slice_dim 3
slice_name alternating_increasing
slice_code 3
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.998962 0.027163 0.058431 108.412506
qto_xyz:2 0.029374 1.998342 0.075949 -98.250397
qto_xyz:3 0.057351 -0.076768 1.997703 -47.447166
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.998962 0.027163 0.058431 108.412506
sto_xyz:2 0.029374 1.998341 0.075949 -98.250397
sto_xyz:3 0.057351 -0.076768 1.997703 -47.447166
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip TE=30;Time=143732.020;phase=1
aux_file SMS_MGH_V2.1;_MB=3;_FOV