360 research outputs found
Motion Compensated Self Supervised Deep Learning for Highly Accelerated 3D Ultrashort Echo Time Pulmonary MRI
Purpose: To investigate motion compensated, self-supervised, model based deep
learning (MBDL) as a method to reconstruct free breathing, 3D Pulmonary
ultrashort echo time (UTE) acquisitions.
Theory and Methods: A self-supervised eXtra Dimension MBDL architecture
(XD-MBDL) was developed that combined respiratory states to reconstruct a
single high-quality 3D image. Non-rigid, GPU based motion fields were
incorporated into this architecture by estimating motion fields from a low
resolution motion resolved (XD-GRASP) iterative reconstruction. Motion
Compensated XD-MBDL was evaluated on lung UTE datasets with and without
contrast and was compared to constrained reconstructions and variants of
self-supervised MBDL that do not consider respiratory motion.
Results: Images reconstructed using XD-MBDL demonstrate improved image
quality as measured by apparent SNR, CNR and visual assessment relative to
self-supervised MBDL approaches that do not account for dynamic respiratory
states, XD-GRASP and a recently proposed motion compensated iterative
reconstruction strategy (iMoCo). Additionally, XD-MBDL reduced reconstruction
time relative to both XD-GRASP and iMoCo.
Conclusion: A method was developed to allow self-supervised MBDL to combine
multiple respiratory states to reconstruct a single image. This method was
combined with GPU-based image registration to further improve reconstruction
quality. This approach showed promising results reconstructing a user-selected
respiratory phase from free breathing 3D pulmonary UTE acquisitions
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Advanced H-1 Lung Magnetic Resonance Imaging
Magnetic resonance imaging (MRI) is one of the widely used medical imaging modality, since it can provide both structural and functional assessment in a single imaging session. However, two major challenges should be considered by using MRI for lung imaging. The first challenge is the intrinsic low SNR of H-1 lung MRI due to the low proton density as well as the fast decay of the lung parenchyma signal. And the second challenge is subject motion. To achieve high resolution structural image, MRI requires a long scan time, usually a few minutes or even longer, which make MRI sensitive to subject motion. To address the first challenge, ultra-short echo time (UTE) MRI sequence is used to capture the lung parenchyma signal before decay. As for subject motion, two major strategies are widely used. One strategy is fast breath-holding scan, the subjects are asked to hold their breaths for a short duration, and the fast 3D MR sequence would be used to acquire data within that duration. This dissertation proposes a new acquisition scheme based on the standard UTE sequence, which largely increases the encoding efficiency and improves the breath-holding scan images. The other is free breathing scan with motion correction. The subjects are allowed to breathe during the MR acquisition. After the acquisition, the motion corrupted data would go through the motion correction step to reconstruct the motion free images. In this dissertation, two novel motion corrected reconstruction strategies are proposed to incorporate the motion modeling and compensation into the reconstruction to get high SNR motion corrected 3D and 4D images. When translating the developed techniques to the clinical studies, specifically for pediatric and neonatal studies, more practical problems need to be considered, such as smaller but finer anatomy to image, the different respiratory patterns of the young subjects etc. This dissertation proposes a 5-minute free breathing UTE MRI strategy to achieve a 3D high resolution motion free lung image for pediatric and neonatal studies
Non-Rigid Groupwise Registration for Motion Estimation and Compensation in Compressed Sensing Reconstruc- tion of Breath-Hold Cardiac Cine MRI
Purpose: Compressed sensing methods with motion estimation and compensation techniques
have been proposed for the reconstruction of accelerated dynamic MRI. However, artifacts that
naturally arise in compressed sensing reconstruction procedures hinder the estimation of motion
from reconstructed images, especially at high acceleration factors. This work introduces a robust
groupwise non-rigid motion estimation technique applied to the compressed sensing reconstruction
of dynamic cardiac cine MRI sequences.
Theory and Methods: A spatio-temporal regularized, groupwise, non-rigid registration method
based on a B-splines deformation model and a least squares metric is used to estimate and to
compensate the movement of the heart in breath-hold cine acquisitions and to obtain a quasi-static
sequence with highly sparse representation in temporally transformed domains.
Results: Short axis in vivo datasets are used for validation, both original multi-coil as well as
DICOM data. Fully sampled data were retrospectively undersampled with various acceleration
factors and reconstructions were compared with the two well-known methods k-t FOCUSS and
MASTeR. The proposed method achieves higher signal to error ratio and structure similarity index
for medium to high acceleration factors.
Conclusions: Reconstruction methods based on groupwise registration show higher quality recon-
structions for cardiac cine images than the pairwise counterparts tested
Structured low-rank methods for robust 3D multi-shot EPI
Magnetic resonance imaging (MRI) has inherently slow acquisition speed, and Echo-Planar Imaging (EPI), as an efficient acquisition scheme, has been widely used in functional magnetic resonance imaging (fMRI) where an image series with high temporal resolution is needed to measure neuronal activity. Recently, 3D multi-shot EPI which samples data from an entire 3D volume with repeated shots has been drawing growing interest for fMRI with its high isotropic spatial resolution, particularly at ultra-high fields. However, compared to single-shot EPI, multi-shot EPI is sensitive to any inter-shot instabilities, e.g., subject movement and even physiologically induced field fluctuations. These inter-shot inconsistencies can greatly negate the theoretical benefits of 3D multi-shot EPI over conventional 2D multi-slice acquisitions.
Structured low-rank image reconstruction which regularises under-sampled image reconstruction by exploiting the linear dependencies in MRI data has been successfully demonstrated in a variety of applications. In this thesis, a structured low-rank reconstruction method is optimised for 3D multi-shot EPI imaging together with a dedicated sampling pattern termed seg-CAIPI, in order to enhance the robustness to physiological fluctuations and improve the temporal stability of 3D multi-shot EPI for fMRI at 7T. Moreover, a motion compensated structured low-rank reconstruction framework is also presented for robust 3D multi-shot EPI which further takes into account inter-shot instabilities due to bulk motion. Lastly, this thesis also investigates into the improvement of structured low-rank reconstruction from an algorithmic perspective and presents the locally structured low-rank reconstruction scheme
Complementary Time-Frequency Domain Networks for Dynamic Parallel MR Image Reconstruction
Purpose: To introduce a novel deep learning based approach for fast and
high-quality dynamic multi-coil MR reconstruction by learning a complementary
time-frequency domain network that exploits spatio-temporal correlations
simultaneously from complementary domains.
Theory and Methods: Dynamic parallel MR image reconstruction is formulated as
a multi-variable minimisation problem, where the data is regularised in
combined temporal Fourier and spatial (x-f) domain as well as in
spatio-temporal image (x-t) domain. An iterative algorithm based on variable
splitting technique is derived, which alternates among signal de-aliasing steps
in x-f and x-t spaces, a closed-form point-wise data consistency step and a
weighted coupling step. The iterative model is embedded into a deep recurrent
neural network which learns to recover the image via exploiting spatio-temporal
redundancies in complementary domains.
Results: Experiments were performed on two datasets of highly undersampled
multi-coil short-axis cardiac cine MRI scans. Results demonstrate that our
proposed method outperforms the current state-of-the-art approaches both
quantitatively and qualitatively. The proposed model can also generalise well
to data acquired from a different scanner and data with pathologies that were
not seen in the training set.
Conclusion: The work shows the benefit of reconstructing dynamic parallel MRI
in complementary time-frequency domains with deep neural networks. The method
can effectively and robustly reconstruct high-quality images from highly
undersampled dynamic multi-coil data ( and yielding 15s
and 10s scan times respectively) with fast reconstruction speed (2.8s). This
could potentially facilitate achieving fast single-breath-hold clinical 2D
cardiac cine imaging.Comment: Accepted by Magnetic Resonance in Medicin
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