Fieldmap estimation

Direct B0 mapping sequences

When the fieldmap is directly measured with a prescribed sequence (such as SE), we only need to calculate the corresponding B-Spline coefficients to adapt the fieldmap to the TOPUP tool. This procedure is described with more detail here.

This corresponds to the section 8.9.3 –fieldmap image (and one magnitude image)– of the BIDS specification.

fmriprep.workflows.fieldmap.fmap.init_fmap_wf(reportlets_dir, omp_nthreads, fmap_bspline, name=’fmap_wf’)[source]

Fieldmap workflow - when we have a sequence that directly measures the fieldmap we just need to mask it (using the corresponding magnitude image) to remove the noise in the surrounding air region, and ensure that units are Hz.

../_images/estimation-1.png

(Source code, png, svg, pdf)

Phase-difference B0 estimation

The field inhomogeneity inside the scanner (fieldmap) is proportional to the phase drift between two subsequent GRE sequence.

Fieldmap preprocessing workflow for fieldmap data structure 8.9.1 in BIDS 1.0.0: one phase diff and at least one magnitude image

fmriprep.workflows.fieldmap.phdiff.init_phdiff_wf(reportlets_dir, name=’phdiff_wf’)[source]

Estimates the fieldmap using a phase-difference image and one or more magnitude images corresponding to two or more GRE acquisitions. The original code was taken from nipype.

../_images/estimation-2.png

(Source code, png, svg, pdf)

Outputs:

outputnode.fmap_ref - The average magnitude image, skull-stripped
outputnode.fmap_mask - The brain mask applied to the fieldmap
outputnode.fmap - The estimated fieldmap in Hz
fmriprep.workflows.fieldmap.phdiff.phdiff2fmap(in_file, delta_te, out_file=None)[source]

Converts the input phase-difference map into a fieldmap in Hz, using the eq. (1) of [Hutton2002]:

\[\Delta B_0 (\text{T}^{-1}) = \frac{\Delta \Theta}{2\pi\gamma \Delta\text{TE}}\]

In this case, we do not take into account the gyromagnetic ratio of the proton (\(\gamma\)), since it will be applied inside TOPUP:

\[\Delta B_0 (\text{Hz}) = \frac{\Delta \Theta}{2\pi \Delta\text{TE}}\]
[Hutton2002]Hutton et al., Image Distortion Correction in fMRI: A Quantitative Evaluation, NeuroImage 16(1):217-240, 2002. doi:10.1006/nimg.2001.1054.