Hello,
Please could I get some advice with solving two errors?
[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)^[[39m
./sub-109S4594/ses-20160502/func/sub-109S4594_ses-20160502_task-rest_bold.nii.gz
"SliceTiming" value/s contains invalid value as it is greater than RepetitionTime. SliceTiming values should be in seconds not milliseconds (common mistake).
The associated .json file looks like the below, and it appears slice timing is in seconds:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.722,
"Manufacturer": "GE",
"ManufacturersModelName": "Signa_HDxt",
"InstitutionName": "HOWARD_UNIVERSITY",
"DeviceSerialNumber": "613ILhuMDTcyYkk9.SUZ.Qk",
"PatientPosition": "HFS",
"SoftwareVersions": "24_LX_MR_Software_release:HD16.0_V02_1131.a",
"MRAcquisitionType": "2D",
"SeriesDescription": "AXIAL_RS_fMRI_(EYES_OPEN)",
"ProtocolName": "AXIAL_RS_fMRI_(EYES_OPEN)",
"ScanningSequence": "EP_GR",
"SequenceVariant": "SS",
"ScanOptions": "MP_GEMS_EPI_GEMS",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"OTHER"
],
"SeriesNumber": 5,
"AcquisitionTime": "10:23:59.000000",
"AcquisitionNumber": 1,
"SliceThickness": 3.3,
"SpacingBetweenSlices": 3.3,
"SAR": 0.184911,
"EchoTime": 0.03,
"RepetitionTime": 2.925,
"FlipAngle": 90,
"PhaseEncodingPolarityGE": "Flipped",
"CoilString": "8HRBRAIN",
"PercentPhaseFOV": 100,
"AcquisitionMatrixPE": 64,
"ReconMatrixPE": 64,
"EffectiveEchoSpacing": 0.000728,
"TotalReadoutTime": 0.045864,
"PixelBandwidth": 7812.5,
"PhaseEncodingDirection": "j",
"SliceTiming": [
4.329,
1.404,
5.733,
2.808,
4.212,
1.287,
5.616,
2.691,
4.095,
1.17,
5.499,
2.574,
3.978,
1.053,
5.382,
2.457,
3.861,
0.936,
5.265,
2.34,
3.744,
0.819,
5.148,
2.223,
3.627,
0.702,
5.031,
2.106,
3.51,
0.585,
4.914,
1.989,
3.393,
0.468,
4.797,
1.872,
3.276,
0.351,
4.68,
1.755,
3.159,
0.234,
4.563,
1.638,
3.042,
0.117,
4.446,
1.521,
2.925,
0
],
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
1,
0
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0",
"Dcm2bidsVersion": "2.1.4"
}
-
[ERR] NIfTI file's header is missing time dimension information. (code: 75 - NIFTI_PIXDIM4). I did not convert these and don’t have the Dicoms so unsure if I can solve it?
The associated headers look like:
sizeof_hdr : 348
data_type : b''
db_name : b''
extents : 0
session_error : 0
regular : b'r'
dim_info : 57
dim : [ 3 80 80 365 1 1 1 1]
intent_p1 : 0.0
intent_p2 : 0.0
intent_p3 : 0.0
intent_code : none
datatype : int16
bitpix : 16
slice_start : 0
pixdim : [-1. 2.94 2.94 3.31 3. 0. 0. 0. ]
vox_offset : 0.0
scl_slope : nan
scl_inter : nan
slice_end : 0
slice_code : unknown
xyzt_units : 10
cal_max : 0.0
cal_min : 0.0
slice_duration : 0.0
toffset : 0.0
glmax : 0
glmin : 0
descrip : b'TE=30;Time=0.000'
aux_file : b''
qform_code : scanner
sform_code : scanner
quatern_b : 0.0
quatern_c : 1.0
quatern_d : 0.0
qoffset_x : 116.30556
qoffset_y : -99.12399
qoffset_z : -70.06402
srow_x : [ -2.94 0. -0. 116.31]
srow_y : [ -0. 2.94 -0. -99.12]
srow_z : [ 0. 0. 3.31 -70.06]
intent_name : b''
magic : b'n+1'
and
sizeof_hdr : 348
data_type : b''
db_name : b''
extents : 0
session_error : 0
regular : b'r'
dim_info : 57
dim : [ 3 64 64 15 1 1 1 1]
intent_p1 : 0.0
intent_p2 : 0.0
intent_p3 : 0.0
intent_code : none
datatype : int16
bitpix : 16
slice_start : 0
pixdim : [-1. 3.31 3.31 6.62 3. 0. 0. 0. ]
vox_offset : 0.0
scl_slope : nan
scl_inter : nan
slice_end : 0
slice_code : unknown
xyzt_units : 10
cal_max : 0.0
cal_min : 0.0
slice_duration : 0.0
toffset : 0.0
glmax : 0
glmin : 0
descrip : b'TE=30;Time=93532.450'
aux_file : b''
qform_code : scanner
sform_code : scanner
quatern_b : 0.0
quatern_c : 1.0
quatern_d : 0.0
qoffset_x : 107.208916
qoffset_y : -107.971535
qoffset_z : -65.90747
srow_x : [ -3.31 0. -0. 107.21]
srow_y : [ -0. 3.31 -0. -107.97]
srow_z : [ 0. 0. 6.62 -65.91]
intent_name : b''
magic : b'n+1'
Thank you very much for any help!