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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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zjjdcrn
November 19, 2019 12:07PM
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":[
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Attachments:
open | download - AP.png (118.8 KB)
open | download - PA.png (118.8 KB)
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Subject Author Posted

b0 field map distortion correction Attachments

zjjdcrn November 19, 2019 12:07PM

Re: b0 field map distortion correction

rick reynolds December 09, 2019 05:16PM