Getting EchoTime1 and EchoTime2 parameters for fmriprep from DICOM header?

fmriprep
bids

#1

Hi,

I apologize if this question is a bit basic, I am a noob at neuroimaging. A collaborator sent us a dataset that includes a B0 map, acquired using a Phillips 3T scanner, which I would like to use in the pipeline. I know that to use the phase maps in fmriprep I need to include EchoTime1 and EchoTime2, or EchoTimeDifference. Do you know where I can find this parameter from the DICOM header?

Thank you!!!

In case it helps, I’m including the JSON file I get from covering using dcm2bids, and the output from fslhd of one of the images:

JSON:
{
“Modality”: “MR”,
“MagneticFieldStrength”: 3,
“Manufacturer”: “Philips”,
“ManufacturersModelName”: “Achieva”,
“InstitutionName”: “XXXX”,
“DeviceSerialNumber”: “17240”,
“StationName”: “XXXX_3T”,
“ProcedureStepDescription”: “30588_123123”,
“SoftwareVersions”: “5.1.7_5.1.7.1”,
“SeriesDescription”: “Ax-B0map”,
“ProtocolName”: “WIP_Ax-B0map_CLEAR”,
“ScanningSequence”: “RM”,
“SequenceVariant”: “SS”,
“ScanOptions”: “OTHER”,
“ImageType”: [“ORIGINAL”, “PRIMARY”, “B0”, “MAP”, “B0”, “UNSPECIFIED”],
“AcquisitionTime”: “16:16:47.310000”,
“AcquisitionNumber”: 10,
“PhilipsRescaleSlope”: 0.2442,
“PhilipsRescaleIntercept”: -500,
“PhilipsScaleSlope”: 4.095,
“UsePhilipsFloatNotDisplayScaling”: 1,
“RepetitionTime”: 0.351895,
“FlipAngle”: 30,
“AcquisitionMatrixPE”: 96,
“PhaseEncodingSteps”: 96,
“PercentPhaseFOV”: 100,
“ConversionSoftware”: “dcm2niix”,
“ConversionSoftwareVersion”: “v1.0.20170821 (OpenJPEG build) GCC4.8.4”
}

FSLHD OUTPUT:

filename ~/123123–Ax-B0map–RM–1001.nii.gz

sizeof_hdr 348
data_type INT16
dim0 4
dim1 96
dim2 96
dim3 50
dim4 2
dim5 0
dim6 0
dim7 0
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.000000
pixdim1 2.500000
pixdim2 2.500000
pixdim3 2.500000
pixdim4 0.351895
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.244202
scl_inter -499.999939
phase_dim 1
freq_dim 2
slice_dim 3
slice_name Unknown
slice_code 0
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 -2.497644 -0.089964 0.060653 120.920654
qto_xyz:2 -0.091702 2.497276 -0.072140 -98.169174
qto_xyz:3 0.057991 0.074297 2.498223 -40.707603
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 -2.497644 -0.089963 0.060664 120.920654
sto_xyz:2 -0.091702 2.497276 -0.072140 -98.169174
sto_xyz:3 0.058002 0.074297 2.498222 -40.707603
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=0;Time=161647.310
aux_file


#2

The piece of metadata you need is not in the information you provided. I would recommend contacting your collaborators to obtain this information (the people who acquired the data know these things best). More about fieldmaps is in section 8.9 of the BIDS specification.


#3

You may want to try out the latest dcm2niix pre-release which can glean more information from Phiips PAR/REC and enhanced DICOM images. I do not have access to Philips hardware, so please test carefully.