Dear AFNI Experts,
I am analyzing a fMRI dataset collected by others, in which they provided field map images to do distortion correction. Have not done this before, luckily I found the program epi_b0_correct.py, which was just added in afni. But I got confused about several questions:
1. According to a webpage describing field map correction, there are different kinds of field map images: phase map(use in SPM toolbox), magnitude map(used in FSL TOPUP). And think the images in current dataset are magnitude map (please see attached), which were collected using Siemens with epse2d1_80. There is one volume of AP direction map and one volume of PA direction map for each run of the epi images. So could I use these to create the phase map as the frequency input of epi_b0_correct.py?
2. If I could use this, should I do the correction before register? or I should do this with all other space transformation in one time?
Thanks!!!
Below is the file for sequence protocol
"Modality":"MR",
"MagneticFieldStrength":3,
"ImagingFrequency":123.223,
"Manufacturer":"Siemens",
"ManufacturersModelName":"TrioTim",
"InstitutionName":"Caltech_Tim32",
"SoftwareVersions":"syngo_MR_B17",
"MRAcquisitionType":"2D",
"SeriesDescription":"SE_EPI_Fieldmap_Neg",
"ProtocolName":"SE_EPI_Fieldmap_Neg",
"ScanningSequence":"EP",
"SequenceVariant":"SK",
"ScanOptions":"FS",
"SequenceName":"epse2d1_80",
"ImageType":[
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"MOSAIC"
],
"SeriesNumber":10,
"AcquisitionTime":"13:55:38.332500",
"AcquisitionNumber":1,
"SliceThickness":2.5,
"SpacingBetweenSlices":2.5,
"SAR":0.369622,
"EchoTime":0.05,
"RepetitionTime":4.8,
"FlipAngle":90,
"PartialFourier":1,
"BaseResolution":80,
"ShimSetting":[
9524,
-10487,
15763,
564,
-11,
300,
-153,
-176
],
"TxRefAmp":311.684,
"PhaseResolution":1,
"ReceiveCoilName":"32Ch_Head",
"CoilString":"C:HEA;HEP",
"PulseSequenceDetails":"%CustomerSeq%_cmrr_mbep2d_se",
"PercentPhaseFOV":100,
"PhaseEncodingSteps":80,
"AcquisitionMatrixPE":80,
"ReconMatrixPE":80,
"BandwidthPerPixelPhaseEncode":23.148,
"EffectiveEchoSpacing":0.000540003,
"DerivedVendorReportedEchoSpacing":0.000540003,
"TotalReadoutTime":0.0426603,
"PixelBandwidth":2404,
"DwellTime":2.6e-06,
"PhaseEncodingDirection":"j",
"SliceTiming":[
