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PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

Research output: Contribution to journalArticle

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PVR : Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI. / Alansary, Amir; Rajchl, Martin; McDonagh, Steven G.; Murgasova, Maria; Damodaram, Mellisa; Lloyd, David F.A.; Davidson, Alice; Rutherford, Mary; Hajnal, Joseph V.; Rueckert, Daniel; Kainz, Bernhard.

In: IEEE Transactions on Medical Imaging, 01.09.2017.

Research output: Contribution to journalArticle

Harvard

Alansary, A, Rajchl, M, McDonagh, SG, Murgasova, M, Damodaram, M, Lloyd, DFA, Davidson, A, Rutherford, M, Hajnal, JV, Rueckert, D & Kainz, B 2017, 'PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI', IEEE Transactions on Medical Imaging. https://doi.org/10.1109/TMI.2017.2737081

APA

Alansary, A., Rajchl, M., McDonagh, S. G., Murgasova, M., Damodaram, M., Lloyd, D. F. A., ... Kainz, B. (2017). PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI. IEEE Transactions on Medical Imaging. https://doi.org/10.1109/TMI.2017.2737081

Vancouver

Alansary A, Rajchl M, McDonagh SG, Murgasova M, Damodaram M, Lloyd DFA et al. PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI. IEEE Transactions on Medical Imaging. 2017 Sep 1. https://doi.org/10.1109/TMI.2017.2737081

Author

Alansary, Amir ; Rajchl, Martin ; McDonagh, Steven G. ; Murgasova, Maria ; Damodaram, Mellisa ; Lloyd, David F.A. ; Davidson, Alice ; Rutherford, Mary ; Hajnal, Joseph V. ; Rueckert, Daniel ; Kainz, Bernhard. / PVR : Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI. In: IEEE Transactions on Medical Imaging. 2017.

Bibtex Download

@article{3e4e1049a2f2459296337c5d7e03e148,
title = "PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI",
abstract = "In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR’s computational overhead compared to standard methods and observe improved reconstruction accuracy in the presence of affine motion artifacts compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. We further evaluate the distance error for selected anatomical landmarks in the fetal head, as well as calculating the mean and maximum displacements resulting from automatic non-rigid registration to a motion-free ground truth image. These experiments demonstrate a successful application of PVR motion compensation to the whole fetal body, uterus and placenta.",
keywords = "Correlation, Fetal Magnetic Resonance Imaging, GPU acceleration, Image reconstruction, Image Reconstruction, Image resolution, Magnetic resonance imaging, Motion Correction, Super-Resolution, Three-dimensional displays, Transmission line matrix methods, Two dimensional displays",
author = "Amir Alansary and Martin Rajchl and McDonagh, {Steven G.} and Maria Murgasova and Mellisa Damodaram and Lloyd, {David F.A.} and Alice Davidson and Mary Rutherford and Hajnal, {Joseph V.} and Daniel Rueckert and Bernhard Kainz",
year = "2017",
month = "9",
day = "1",
doi = "10.1109/TMI.2017.2737081",
language = "English",
journal = "IEEE Transactions on Medical Imaging",
issn = "0278-0062",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - PVR

T2 - Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

AU - Alansary, Amir

AU - Rajchl, Martin

AU - McDonagh, Steven G.

AU - Murgasova, Maria

AU - Damodaram, Mellisa

AU - Lloyd, David F.A.

AU - Davidson, Alice

AU - Rutherford, Mary

AU - Hajnal, Joseph V.

AU - Rueckert, Daniel

AU - Kainz, Bernhard

PY - 2017/9/1

Y1 - 2017/9/1

N2 - In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR’s computational overhead compared to standard methods and observe improved reconstruction accuracy in the presence of affine motion artifacts compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. We further evaluate the distance error for selected anatomical landmarks in the fetal head, as well as calculating the mean and maximum displacements resulting from automatic non-rigid registration to a motion-free ground truth image. These experiments demonstrate a successful application of PVR motion compensation to the whole fetal body, uterus and placenta.

AB - In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR’s computational overhead compared to standard methods and observe improved reconstruction accuracy in the presence of affine motion artifacts compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. We further evaluate the distance error for selected anatomical landmarks in the fetal head, as well as calculating the mean and maximum displacements resulting from automatic non-rigid registration to a motion-free ground truth image. These experiments demonstrate a successful application of PVR motion compensation to the whole fetal body, uterus and placenta.

KW - Correlation

KW - Fetal Magnetic Resonance Imaging

KW - GPU acceleration

KW - Image reconstruction

KW - Image Reconstruction

KW - Image resolution

KW - Magnetic resonance imaging

KW - Motion Correction

KW - Super-Resolution

KW - Three-dimensional displays

KW - Transmission line matrix methods

KW - Two dimensional displays

UR - http://www.scopus.com/inward/record.url?scp=85029160935&partnerID=8YFLogxK

U2 - 10.1109/TMI.2017.2737081

DO - 10.1109/TMI.2017.2737081

M3 - Article

AN - SCOPUS:85029160935

JO - IEEE Transactions on Medical Imaging

JF - IEEE Transactions on Medical Imaging

SN - 0278-0062

ER -

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