Functional MRI (fMRI) data acquired using echo-planar imaging (EPI) are highly distorted by magnetic field inhomogeneities. Distortion and differences in image contrast between EPI and T1-weighted and T2-weighted (T1w/T2w) images makes their alignment a challenge. Typically, field map data are used to correct EPI distortions. Alignments achieved with field maps can vary greatly and depends on the quality of field map data. However, many public datasets lack field map data entirely. Additionally, reliable field map data is often difficult to acquire in high-motion pediatric or developmental cohorts. To address this, we developed Synth, a software package for distortion correction and cross-modal image registration that does not require field map data. Synth combines information from T1w and T2w anatomical images to construct an idealized undistorted synthetic image with similar contrast properties to EPI data. This synthetic image acts as an effective reference for individual-specific distortion correction. Using pediatric (ABCD: Adolescent Brain Cognitive Development) and adult (MSC: Midnight Scan Club; HCP: Human Connectome Project) data, we demonstrate that Synth performs comparably to field map distortion correction approaches, and often outperforms them. Field map-less distortion correction with Synth allows accurate and precise registration of fMRI data with missing or corrupted field map information.

fMRI

EPI

Distortion correction

Field map

Registration

The ABCD data repository grows and changes over time. The ABCD data used in this report came from ABCD collection 3165 and the Annual Release 2.0, http://dx.doi.org/10.15154/1503209. The MSC dataset used in this report can downloaded at can be found on OpenNeuro.org, http://dx.doi.org/10.18112/openneuro.ds000224.v1.0.3. HCP data can be downloaded at https://humanconnectome.org/study/hcp-young-adult.

© 2023 The Author(s). Published by Elsevier Ltd.