Automated slice-specific z-shimming for functional magnetic resonance imaging of the human spinal cord

TY - JOUR

T1 - Automated slice-specific z-shimming for functional magnetic resonance imaging of the human spinal cord

AU - Kaptan, Merve

AU - Vannesjo, S Johanna

AU - Mildner, Toralf

AU - Horn, Ulrike

AU - Hartley-Davies, Ronald

AU - Oliva, Valeria

AU - Brooks, Jonathan C W

AU - Weiskopf, Nikolaus

AU - Finsterbusch, Jürgen

AU - Eippert, Falk

N1 - © 2022 The Authors. Human Brain Mapping published by Wiley Periodicals LLC.

PY - 2022/12/15

Y1 - 2022/12/15

N2 - Functional magnetic resonance imaging (fMRI) of the human spinal cord faces many challenges, such as signal loss due to local magnetic field inhomogeneities. This issue can be addressed with slice-specific z-shimming, which compensates for the dephasing effect of the inhomogeneities using a slice-specific gradient pulse. Here, we aim to address outstanding issues regarding this technique by evaluating its effects on several aspects that are directly relevant for spinal fMRI and by developing two automated procedures in order to improve upon the time-consuming and subjective nature of manual selection of z-shims: one procedure finds the z-shim that maximizes signal intensity in each slice of an EPI reference-scan and the other finds the through-slice field inhomogeneity for each EPI-slice in field map data and calculates the required compensation gradient moment. We demonstrate that the beneficial effects of z-shimming are apparent across different echo times, hold true for both the dorsal and ventral horn, and are also apparent in the temporal signal-to-noise ratio (tSNR) of EPI time-series data. Both of our automated approaches were faster than the manual approach, lead to significant improvements in gray matter tSNR compared to no z-shimming and resulted in beneficial effects that were stable across time. While the field-map-based approach performed slightly worse than the manual approach, the EPI-based approach performed as well as the manual one and was furthermore validated on an external corticospinal data-set (N > 100). Together, automated z-shimming may improve the data quality of future spinal fMRI studies and lead to increased reproducibility in longitudinal studies.

AB - Functional magnetic resonance imaging (fMRI) of the human spinal cord faces many challenges, such as signal loss due to local magnetic field inhomogeneities. This issue can be addressed with slice-specific z-shimming, which compensates for the dephasing effect of the inhomogeneities using a slice-specific gradient pulse. Here, we aim to address outstanding issues regarding this technique by evaluating its effects on several aspects that are directly relevant for spinal fMRI and by developing two automated procedures in order to improve upon the time-consuming and subjective nature of manual selection of z-shims: one procedure finds the z-shim that maximizes signal intensity in each slice of an EPI reference-scan and the other finds the through-slice field inhomogeneity for each EPI-slice in field map data and calculates the required compensation gradient moment. We demonstrate that the beneficial effects of z-shimming are apparent across different echo times, hold true for both the dorsal and ventral horn, and are also apparent in the temporal signal-to-noise ratio (tSNR) of EPI time-series data. Both of our automated approaches were faster than the manual approach, lead to significant improvements in gray matter tSNR compared to no z-shimming and resulted in beneficial effects that were stable across time. While the field-map-based approach performed slightly worse than the manual approach, the EPI-based approach performed as well as the manual one and was furthermore validated on an external corticospinal data-set (N > 100). Together, automated z-shimming may improve the data quality of future spinal fMRI studies and lead to increased reproducibility in longitudinal studies.

KW - Humans

KW - Echo-Planar Imaging/methods

KW - Artifacts

KW - Image Processing, Computer-Assisted/methods

KW - Reproducibility of Results

KW - Magnetic Resonance Imaging/methods

KW - Spinal Cord/diagnostic imaging

KW - Brain/diagnostic imaging

U2 - 10.1002/hbm.26018

DO - 10.1002/hbm.26018

M3 - SCORING: Journal article

C2 - 35938527

VL - 43

SP - 5389

EP - 5407

JO - HUM BRAIN MAPP

JF - HUM BRAIN MAPP

SN - 1065-9471

IS - 18

ER -