Assessing methods for geometric distortion compensation in 7 T gradient echo functional MRI data

• Published in: Human brain mapping Vol. 42; no. 13; pp. 4205 - 4223
• Main Authors: Schallmo, Michael‐Paul, Weldon, Kimberly B., Burton, Philip C., Sponheim, Scott R., Olman, Cheryl A.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.09.2021
• Subjects: 7 Tesla; Adult; B0 inhomogeneity; Bandwidths; Brain - diagnostic imaging; Brain - physiopathology; Compensation; Distortion; distortion compensation; echo planar imaging; Echo-Planar Imaging - methods; Echo-Planar Imaging - standards; Family; Female; field map; Field strength; Functional magnetic resonance imaging; functional MRI; Functional Neuroimaging - methods; Functional Neuroimaging - standards; Human performance; Humans; Magnetic fields; Magnetic resonance imaging; Male; Mapping; Medical imaging; Methods; Middle Aged; Neuroimaging; Prefrontal cortex; Psychotic Disorders - diagnostic imaging; Psychotic Disorders - physiopathology; Quality assessment; Registration; Schizophrenia - diagnostic imaging; Schizophrenia - physiopathology; echo planar imaging; functional MRI; B0 inhomogeneity; distortion compensation; field map; 7 Tesla
• ISSN: 1065-9471; 1097-0193
• DOI: 10.1002/hbm.25540

Echo planar imaging (EPI) is widely used in functional and diffusion‐weighted MRI, but suffers from significant geometric distortions in the phase encoding direction caused by inhomogeneities in the static magnetic field (B0). This is a particular challenge for EPI at very high field (≥7 T), as distortion increases with higher field strength. A number of techniques for distortion correction exist, including those based on B0 field mapping and acquiring EPI scans with opposite phase encoding directions. However, few quantitative comparisons of distortion compensation methods have been performed using human EPI data, especially at very high field. Here, we compared distortion compensation using B0 field maps and opposite phase encoding scans in two different software packages (FSL and AFNI) applied to 7 T gradient echo (GE) EPI data from 31 human participants. We assessed distortion compensation quality by quantifying alignment to anatomical reference scans using Dice coefficients and mutual information. Performance between FSL and AFNI was equivalent. In our whole‐brain analyses, we found superior distortion compensation using GE scans with opposite phase encoding directions, versus B0 field maps or spin echo (SE) opposite phase encoding scans. However, SE performed better when analyses were limited to ventromedial prefrontal cortex, a region with substantial dropout. Matching the type of opposite phase encoding scans to the EPI data being corrected (e.g., SE‐to‐SE) also yielded better distortion correction. While the ideal distortion compensation approach likely varies depending on methodological differences across experiments, this study provides a framework for quantitative comparison of different distortion compensation methods. We compared distortion compensation using B0 field maps and opposite phase encoding scans in two different software packages (FSL and AFNI) applied to 7 T gradient echo (GE) echo planar imaging data from 31 human participants. We assessed distortion compensation quality by quantifying alignment to anatomical reference scans using Dice coefficients and mutual information. In our whole‐brain analyses, we found superior distortion compensation using GE scans with opposite phase encoding directions, versus B0 field maps or spin echo opposite phase encoding scans.