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.

Original language	English
Title of host publication	Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition
Number of pages	3
Publisher	The International Society for Magnetic Resonance in Medicine
Publication date	2020
Pages	1-3
Article number	3667
Publication status	Published - 2020
Event	ISMRM & SMRT Virtual Conference & Exhibition 2020 - Virtual conference Duration: 8 Aug 2020 → 14 Aug 2020 https://www.ismrm.org/20m/

Conference

Conference	ISMRM & SMRT Virtual Conference & Exhibition 2020
Location	Virtual conference
Period	08/08/2020 → 14/08/2020
Internet address	https://www.ismrm.org/20m/

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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. In Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition (pp. 1-3). Article 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. p. 1-3 3667.

Research output: Chapter in Book/Report/Conference proceeding › Conference abstract in proceedings › Research › 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. in Proceedings of the 2020 ISMRM & SMRT Virtual Conference & Exhibition., 3667, The International Society for Magnetic Resonance in Medicine, pp. 1-3, ISMRM & SMRT Virtual Conference & Exhibition 2020, 08/08/2020. <https://archive.ismrm.org/2020/3667.html>

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title = "Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer",

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",

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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

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