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

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‐sp...

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Autores principales: Kaptan, Merve, Vannesjo, S. Johanna, Mildner, Toralf, Horn, Ulrike, Hartley‐Davies, Ronald, Oliva, Valeria, Brooks, Jonathan C. W., Weiskopf, Nikolaus, Finsterbusch, Jürgen, Eippert, Falk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704784/
https://www.ncbi.nlm.nih.gov/pubmed/35938527
http://dx.doi.org/10.1002/hbm.26018
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author Kaptan, Merve
Vannesjo, S. Johanna
Mildner, Toralf
Horn, Ulrike
Hartley‐Davies, Ronald
Oliva, Valeria
Brooks, Jonathan C. W.
Weiskopf, Nikolaus
Finsterbusch, Jürgen
Eippert, Falk
author_facet Kaptan, Merve
Vannesjo, S. Johanna
Mildner, Toralf
Horn, Ulrike
Hartley‐Davies, Ronald
Oliva, Valeria
Brooks, Jonathan C. W.
Weiskopf, Nikolaus
Finsterbusch, Jürgen
Eippert, Falk
author_sort Kaptan, Merve
collection PubMed
description 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.
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spelling pubmed-97047842022-11-29 Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord Kaptan, Merve Vannesjo, S. Johanna Mildner, Toralf Horn, Ulrike Hartley‐Davies, Ronald Oliva, Valeria Brooks, Jonathan C. W. Weiskopf, Nikolaus Finsterbusch, Jürgen Eippert, Falk Hum Brain Mapp Technical Report 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. John Wiley & Sons, Inc. 2022-08-08 /pmc/articles/PMC9704784/ /pubmed/35938527 http://dx.doi.org/10.1002/hbm.26018 Text en © 2022 The Authors. Human Brain Mapping published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Report
Kaptan, Merve
Vannesjo, S. Johanna
Mildner, Toralf
Horn, Ulrike
Hartley‐Davies, Ronald
Oliva, Valeria
Brooks, Jonathan C. W.
Weiskopf, Nikolaus
Finsterbusch, Jürgen
Eippert, Falk
Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
title Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
title_full Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
title_fullStr Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
title_full_unstemmed Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
title_short Automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
title_sort automated slice‐specific z‐shimming for functional magnetic resonance imaging of the human spinal cord
topic Technical Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704784/
https://www.ncbi.nlm.nih.gov/pubmed/35938527
http://dx.doi.org/10.1002/hbm.26018
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