How can I tell if I have gradient echo fieldmaps?

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1

Hi everyone,

I see in the changelog for fmriprep 24.1.0 it has improved handling of gradient echo fieldmaps. I was wondering how I can tell if I have these gradient echo fieldmaps.

In my bids directory, for a subject sub-01, their sub-01/fmap/ses-V1 folder contains files:
sub-01_ses-V1_acq-func_dir-AP_run-01_epi.json
sub-01_ses-V1_acq-func_dir-AP_run-01_epi.nii.gz
sub-01_ses-V1_acq-func_dir-PA_run-01_epi.json
sub-01_ses-V1_acq-func_dir-PA_run-01_epi.nii.gz

I see AP and PA fieldmaps - does this mean I have gradient echo fieldmaps? How would I otherwise be able to tell?

Thanks,
Shane

2

Hi @swwalsh1,

In short, you do not have GRE fieldmaps.

GRE Field Maps

GRE field maps, also known as dual-echo gradient-recalled echo sequences, are commonly used to measure the B0 field distortions. They typically provide phase and magnitude images from which a voxelwise map of the magnetic field can be computed.

In BIDS, GRE field maps are organized as follows:

  1. Phase and Magnitude Images:
  • Two magnitude images (e.g., *_magnitude1.nii.gz and *_magnitude2.nii.gz) and one phase difference image (e.g., *_phasediff.nii.gz).
  • The JSON sidecar files (*_phasediff.json, *_magnitude1.json, *_magnitude2.json) include metadata like echo times (EchoTime1, EchoTime2) and other acquisition parameters.
  • Example BIDS structure:
sub-01/
  fmap/
    sub-01_phasediff.nii.gz
    sub-01_phasediff.json
    sub-01_magnitude1.nii.gz
    sub-01_magnitude1.json
    sub-01_magnitude2.nii.gz
    sub-01_magnitude2.json
  1. Usage: These are used for distortion correction, typically for EPI (echo-planar imaging) sequences like fMRI or diffusion MRI.

SE Field Maps (SE-EPI)

SE-EPI field maps, or Spin Echo Echo-Planar Imaging field maps, are another approach. They involve acquiring images with opposite phase-encoding directions (e.g., AP/PA or LR/RL) to estimate the B0 distortions.

In BIDS, SE field maps are organized as:

  1. Two Opposing Phase-Encoded EPI Images:
  • Two separate images acquired with different phase encoding directions, usually indicated in the filename (e.g., _dir-AP.nii.gz and _dir-PA.nii.gz).
  • The JSON sidecar files (*_dir-AP.json, *_dir-PA.json) contain important metadata like PhaseEncodingDirection and TotalReadoutTime.
  • Example BIDS structure:
sub-01/
  fmap/
    sub-01_dir-AP_epi.nii.gz
    sub-01_dir-AP_epi.json
    sub-01_dir-PA_epi.nii.gz
    sub-01_dir-PA_epi.json
  1. Usage: These field maps are used to correct EPI distortions in methods such as topup in FSL, which combines the images to estimate the off-resonance field.

Key Differences

  • GRE Field Maps: Provide a direct measure of the magnetic field inhomogeneity through phase and magnitude images. They are often used with fMRI and diffusion MRI data.
  • SE-EPI Field Maps: Use phase-encoded images to indirectly estimate field distortions and are typically used in cases where you have substantial distortions from susceptibility, like fMRI or diffusion MRI.

Each method has its own strengths. GRE field maps offer direct measurements but can be susceptible to issues like phase wrapping, while SE-EPI field maps are more robust in some situations but require more complex processing.

1 Like
3

Thank you, Steven, for your detailed response!