Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer

Giske  Opheim; Oula Puonti; Jan Ole Pedersen; Vincent Oltman Boer; Ane Kloster; Martin Prener; Helle Juhl Simonsen; Olaf Bjarne Paulson; Lars Hageman Pinborg; Melanie  Ganz

Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer

Giske Opheim, Oula Puonti, Jan Ole Pedersen, Vincent Oltman Boer, Ane Kloster, Martin Prener, Helle Juhl Simonsen, Olaf Bjarne Paulson, Lars Hageman Pinborg, Melanie Ganz

Abstract

Automated cortical segmentations benefit from higher SNR and spatial resolutions on 7T MR images, but are also challenged by B1 inhomogeneities, causing faulty surface inflations primarily in the temporal lobes. We investigated how FreeSurfer outputs were affected by applying eight different preprocessing schemes prior to reconstructions of submillimeter 7T MPRAGE images. The highest segmentation robustness across subjects was obtained by setting bias-field correction FWHM to 60mm and adding light regularization, and additionally performing intensity normalization.

Originalsprog	Engelsk
Titel	Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition
Antal sider	3
Forlag	The International Society for Magnetic Resonance in Medicine
Publikationsdato	2020
Sider	1-3
Artikelnummer	3667
Status	Udgivet - 2020
Begivenhed	ISMRM & SMRT Virtual Conference & Exhibition 2020 - Virtual conference Varighed: 8 aug. 2020 → 14 aug. 2020 https://www.ismrm.org/20m/

Konference

Konference	ISMRM & SMRT Virtual Conference & Exhibition 2020
Lokation	Virtual conference
Periode	08/08/2020 → 14/08/2020
Internetadresse	https://www.ismrm.org/20m/

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https://archive.ismrm.org/2020/3667.html

Citationsformater

Opheim, G., Puonti, O., Pedersen, J. O., Boer, V. O., Kloster, A., Prener, M., Simonsen, H. J., Paulson, O. B., Pinborg, L. H., & Ganz, M. (2020). Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer. I Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition (s. 1-3). Artikel 3667 The International Society for Magnetic Resonance in Medicine. https://archive.ismrm.org/2020/3667.html

Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer. / Opheim, Giske; Puonti, Oula; Pedersen, Jan Ole et al.
Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition. The International Society for Magnetic Resonance in Medicine, 2020. s. 1-3 3667.

Publikation: Bidrag til bog/antologi/rapport › Konferenceabstrakt i proceedings › Forskning › peer review

Opheim, G, Puonti, O, Pedersen, JO, Boer, VO, Kloster, A, Prener, M, Simonsen, HJ, Paulson, OB , Pinborg, LH & Ganz, M 2020, Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer. i Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition., 3667, The International Society for Magnetic Resonance in Medicine, s. 1-3, ISMRM & SMRT Virtual Conference & Exhibition 2020, 08/08/2020. <https://archive.ismrm.org/2020/3667.html>

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abstract = "Automated cortical segmentations benefit from higher SNR and spatial resolutions on 7T MR images, but are also challenged by B1 inhomogeneities, causing faulty surface inflations primarily in the temporal lobes. We investigated how FreeSurfer outputs were affected by applying eight different preprocessing schemes prior to reconstructions of submillimeter 7T MPRAGE images. The highest segmentation robustness across subjects was obtained by setting bias-field correction FWHM to 60mm and adding light regularization, and additionally performing intensity normalization.",

author = "Giske Opheim and Oula Puonti and Pedersen, {Jan Ole} and Boer, {Vincent Oltman} and Ane Kloster and Martin Prener and Simonsen, {Helle Juhl} and Paulson, {Olaf Bjarne} and Pinborg, {Lars Hageman} and Melanie Ganz",

year = "2020",

language = "English",

pages = "1--3",

booktitle = "Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition",

publisher = "The International Society for Magnetic Resonance in Medicine",

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T1 - Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer

AU - Opheim, Giske

AU - Puonti, Oula

AU - Pedersen, Jan Ole

AU - Boer, Vincent Oltman

AU - Kloster, Ane

AU - Prener, Martin

AU - Simonsen, Helle Juhl

AU - Paulson, Olaf Bjarne

AU - Pinborg, Lars Hageman

AU - Ganz, Melanie

PY - 2020

Y1 - 2020

N2 - Automated cortical segmentations benefit from higher SNR and spatial resolutions on 7T MR images, but are also challenged by B1 inhomogeneities, causing faulty surface inflations primarily in the temporal lobes. We investigated how FreeSurfer outputs were affected by applying eight different preprocessing schemes prior to reconstructions of submillimeter 7T MPRAGE images. The highest segmentation robustness across subjects was obtained by setting bias-field correction FWHM to 60mm and adding light regularization, and additionally performing intensity normalization.

AB - Automated cortical segmentations benefit from higher SNR and spatial resolutions on 7T MR images, but are also challenged by B1 inhomogeneities, causing faulty surface inflations primarily in the temporal lobes. We investigated how FreeSurfer outputs were affected by applying eight different preprocessing schemes prior to reconstructions of submillimeter 7T MPRAGE images. The highest segmentation robustness across subjects was obtained by setting bias-field correction FWHM to 60mm and adding light regularization, and additionally performing intensity normalization.

M3 - Conference abstract in proceedings

SP - 1

EP - 3

BT - Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition

PB - The International Society for Magnetic Resonance in Medicine

T2 - ISMRM & SMRT Virtual Conference & Exhibition 2020

Y2 - 8 August 2020 through 14 August 2020

ER -

Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer

Abstract

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