Fast motion compensation and super-resolution from multiple stacks of 2D slices
Author(s)
Kainz, B
Alansary, A
McDonagh, ST
Keraudren, K
Kuklisova-Murgasova, M
Type
Software / Code
Abstract
This tool implements a novel method for the correction of motion artifacts as acquired in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible 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 defined amount of redundant information that is addressed with parallelized patch-wise optimization 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 presence of affine motion artifacts of approximately 30% compared to conventional SVR in synthetic experiments.
Furthermore, we have verified 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. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.
Furthermore, we have verified 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. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.
Version
1.0
Date Issued
2016-11-01
Citation
2016
Copyright Statement
MIT https://opensource.org/licenses/MIT
Sponsor
Engineering and Physical Sciences Research Council (EPSRC)
Engineering & Physical Science Research Council (EPSRC)
Wellcome Trust/EPSRC
Grant Number
EP/N024494/1
EP/N024494/1
NS/A000025/1
Subjects
Magnetic resonance imaing
motion compensation
GPU acceleration
fetal imaging