Susceptibility Distortion Correction (SDC)

Please note that all routines for susceptibility-derived distortion correction have been excised off of fMRIPrep for utilization on other projects (e.g., dMRIPrep). For more detailed documentation on SDC routines, check on


SDC methods usually try to make a good estimate of the field inhomogeneity map. The inhomogeneity map is directly related to the displacement of a given pixel \((x, y, z)\) along the PE direction (\(d_\text{PE}(x, y, z)\)) is proportional to the slice readout time (\(T_\text{ro}\)) and the field inhomogeneity (\(\Delta B_0(x, y, z)\)) as follows ([Jezzard1995], [Hutton2002]):

\[d_\text{PE}(x, y, z) = \gamma \Delta B_0(x, y, z) T_\text{ro} \qquad (1)\]

where \(\gamma\) is the gyromagnetic ratio. Therefore, the displacements map \(d_\text{PE}(x, y, z)\) can be estimated either via estimating the inhomogeneity map \(\Delta B_0(x, y, z)\) or via image registration (see below).

Correction methods

The are five broad families of methodologies for mapping the field:

  1. Phase Encoding POLARity (PEPOLAR; also called blip-up/blip-down; init_pepolar_unwarp_wf()): acquire at least two images with varying PE directions. Hence, the realization of distortion is different between the different acquisitions. The displacements map \(d_\text{PE}(x, y, z)\) is estimated with an image registration process between the different PE acquisitions, regularized by the readout time \(T_\text{ro}\). Corresponds to 8.9.4 of BIDS.

  2. Direct B0 mapping sequences (init_fmap_wf()): some sequences (such as SE) are able to measure the fieldmap \(\Delta B_0(x, y, z)\) directly. Corresponds to section 8.9.3 of BIDS.

  3. Phase-difference B0 mapping (init_phdiff_wf()): to estimate the fieldmap \(\Delta B_0(x, y, z)\), these methods measure the phase evolution in time between two close GRE acquisitions. Corresponds to the sections 8.9.1 and 8.9.2 of the BIDS specification.

  4. “Fieldmap-less” estimation (experimental; init_syn_sdc_wf()): fMRIPrep now experimentally supports displacement field estimation in the absence of fieldmaps via nonlinear registration.

  5. Point-spread function acquisition: Not supported by BIDS, and hence fMRIPrep.

In order to select the appropriate estimation workflow, the input BIDS dataset is first queried to find the available field-mapping techniques (see init_sdc_estimate_wf()). Once the field-map (or the corresponding displacement field) is estimated, the distortion can be accounted for (see init_sdc_unwarp_wf()).

Calculating the effective echo-spacing and total-readout time

To solve (1), all methods (with the exception of the fieldmap-less approach) will require information about the in-plane speed of the EPI scheme used in acquisition by reading either the \(T_\text{ro}\) (total-readout time) or \(t_\text{ees}\) (effective echo-spacing). See corresponding implementations under SDCFlows:

From the phase-difference map to a field map

To solve (1) using a phase-difference map, the field map \(\Delta B_0(x, y, z)\) can be derived from the phase-difference map (phdiff2fmap())



P. Jezzard, R.S. Balaban Correction for geometric distortion in echo planar images from B0 field variations Magn. Reson. Med., 34 (1) (1995), pp. 65-73, doi:10.1002/mrm.1910340111.


Hutton et al., Image Distortion Correction in fMRI: A Quantitative Evaluation, NeuroImage 16(1):217-240, 2002. doi:10.1006/nimg.2001.1054.