1,691 research outputs found
FReSCO: Flow Reconstruction and Segmentation for low-latency Cardiac Output monitoring using deep artifact suppression and segmentation
Purpose: Real-time monitoring of cardiac output (CO) requires low-latency reconstruction and segmentation of real-time phase-contrast MR, which has previously been difficult to perform. Here we propose a deep learning framework for āFReSCOā (Flow Reconstruction and Segmentation for low latency Cardiac Output monitoring). Methods: Deep artifact suppression and segmentation U-Nets were independently trained. Breath-hold spiral phase-contrast MR data (NĀ =Ā 516) were synthetically undersampled using a variable-density spiral sampling pattern and gridded to create aliased data for training of the artifact suppression U-net. A subset of the data (NĀ =Ā 96) was segmented and used to train the segmentation U-net. Real-time spiral phase-contrast MR was prospectively acquired and then reconstructed and segmented using the trained models (FReSCO) at low latency at the scanner in 10 healthy subjects during rest, exercise, and recovery periods. Cardiac output obtained via FReSCO was compared with a reference rest CO and rest and exercise compressed-sensing CO. Results: The FReSCO framework was demonstrated prospectively at the scanner. Beat-to-beat heartrate, stroke volume, and CO could be visualized with a mean latency of 622 ms. No significant differences were noted when compared with reference at rest (biasĀ =Ā ā0.21 Ā± 0.50 L/min, pĀ =Ā 0.246) or compressed sensing at peak exercise (biasĀ =Ā 0.12 Ā± 0.48 L/min, pĀ =Ā 0.458). Conclusions: The FReSCO framework was successfully demonstrated for real-time monitoring of CO during exercise and could provide a convenient tool for assessment of the hemodynamic response to a range of stressors
Retrospective Motion Correction in Magnetic Resonance Imaging of the Brain
Magnetic Resonance Imaging (MRI) is a tremendously useful diagnostic imaging modality that provides outstanding soft tissue contrast. However, subject motion is a significant unsolved problem; motion during image acquisition can cause blurring and distortions in the image, limiting its diagnostic utility. Current techniques for addressing head motion include optical tracking which can be impractical in clinical settings due to challenges associated with camera cross-calibration and marker fixation. Another category of techniques is MRI navigators, which use specially acquired MRI data to track the motion of the head.
This thesis presents two techniques for motion correction in MRI: the first is spherical navigator echoes (SNAVs), which are rapidly acquired k-space navigators. The second is a deep convolutional neural network trained to predict an artefact-free image from motion-corrupted data.
Prior to this thesis, SNAVs had been demonstrated for motion measurement but not motion correction, and they required the acquisition of a 26s baseline scan during which the subject could not move. In this work, a novel baseline approach is developed where the acquisition is reduced to 2.6s. Spherical navigators were interleaved into a spoiled gradient echo sequence (SPGR) on a stand-alone MRI system and a turbo-FLASH sequence (tfl) on a hybrid PET/MRI system to enable motion measurement throughout image acquisition. The SNAV motion measurements were then used to retrospectively correct the image data.
While MRI navigator methods, particularly SNAVs that can be acquired very rapidly, are useful for motion correction, they do require pulse sequence modifications. A deep learning technique may be a more general solution. In this thesis, a conditional generative adversarial network (cGAN) is trained to perform motion correction on image data with simulated motion artefacts. We simulate motion in previously acquired brain images and use the image pairs (corrupted + original) to train the cGAN.
MR image data was qualitatively and quantitatively improved following correction using the SNAV motion estimates. This was also true for the simultaneously acquired MR and PET data on the hybrid system. Motion corrected images were more similar than the uncorrected to the no-motion reference images. The deep learning approach was also successful for motion correction. The trained cGAN was evaluated on 5 subjects; and artefact suppression was observed in all images
Improved 3D MR Image Acquisition and Processing in Congenital Heart Disease
Congenital heart disease (CHD) is the most common type of birth defect, affecting about 1% of the population. MRI is an essential tool in the assessment of CHD, including diagnosis, intervention planning and follow-up. Three-dimensional MRI can provide particularly rich visualization and information. However, it is often complicated by long scan times, cardiorespiratory motion, injection of contrast agents, and complex and time-consuming postprocessing. This thesis comprises four pieces of work that attempt to respond to some of these challenges.
The first piece of work aims to enable fast acquisition of 3D time-resolved cardiac imaging during free breathing. Rapid imaging was achieved using an efficient spiral sequence and a sparse parallel imaging reconstruction. The feasibility of this approach was demonstrated on a population of 10 patients with CHD, and areas of improvement were identified.
The second piece of work is an integrated software tool designed to simplify and accelerate the development of machine learning (ML) applications in MRI research. It also exploits the strengths of recently developed ML libraries for efficient MR image reconstruction and processing.
The third piece of work aims to reduce contrast dose in contrast-enhanced MR angiography (MRA). This would reduce risks and costs associated with contrast agents. A deep learning-based contrast enhancement technique was developed and shown to improve image quality in real low-dose MRA in a population of 40 children and adults with CHD.
The fourth and final piece of work aims to simplify the creation of computational models for hemodynamic assessment of the great arteries. A deep learning technique for 3D segmentation of the aorta and the pulmonary arteries was developed and shown to enable accurate calculation of clinically relevant biomarkers in a population of 10 patients with CHD
Learning associations between clinical information and motion-based descriptors using a large scale MR-derived cardiac motion atlas
The availability of large scale databases containing imaging and non-imaging
data, such as the UK Biobank, represents an opportunity to improve our
understanding of healthy and diseased bodily function. Cardiac motion atlases
provide a space of reference in which the motion fields of a cohort of subjects
can be directly compared. In this work, a cardiac motion atlas is built from
cine MR data from the UK Biobank (~ 6000 subjects). Two automated quality
control strategies are proposed to reject subjects with insufficient image
quality. Based on the atlas, three dimensionality reduction algorithms are
evaluated to learn data-driven cardiac motion descriptors, and statistical
methods used to study the association between these descriptors and non-imaging
data. Results show a positive correlation between the atlas motion descriptors
and body fat percentage, basal metabolic rate, hypertension, smoking status and
alcohol intake frequency. The proposed method outperforms the ability to
identify changes in cardiac function due to these known cardiovascular risk
factors compared to ejection fraction, the most commonly used descriptor of
cardiac function. In conclusion, this work represents a framework for further
investigation of the factors influencing cardiac health.Comment: 2018 International Workshop on Statistical Atlases and Computational
Modeling of the Hear
Detecting respiratory motion artefacts for cardiovascular MRIs to ensure high-quality segmentation
While machine learning approaches perform well on their training domain, they
generally tend to fail in a real-world application. In cardiovascular magnetic
resonance imaging (CMR), respiratory motion represents a major challenge in
terms of acquisition quality and therefore subsequent analysis and final
diagnosis. We present a workflow which predicts a severity score for
respiratory motion in CMR for the CMRxMotion challenge 2022. This is an
important tool for technicians to immediately provide feedback on the CMR
quality during acquisition, as poor-quality images can directly be re-acquired
while the patient is still available in the vicinity. Thus, our method ensures
that the acquired CMR holds up to a specific quality standard before it is used
for further diagnosis. Therefore, it enables an efficient base for proper
diagnosis without having time and cost-intensive re-acquisitions in cases of
severe motion artefacts. Combined with our segmentation model, this can help
cardiologists and technicians in their daily routine by providing a complete
pipeline to guarantee proper quality assessment and genuine segmentations for
cardiovascular scans. The code base is available at
https://github.com/MECLabTUDA/QA_med_data/tree/dev_QA_CMRxMotion
Automatic Multi-Class Cardiovascular Magnetic Resonance Image Quality Assessment using Unsupervised Domain Adaptation in Spatial and Frequency Domains
Population imaging studies rely upon good quality medical imagery before
downstream image quantification. This study provides an automated approach to
assess image quality from cardiovascular magnetic resonance (CMR) imaging at
scale. We identify four common CMR imaging artefacts, including respiratory
motion, cardiac motion, Gibbs ringing, and aliasing. The model can deal with
images acquired in different views, including two, three, and four-chamber
long-axis and short-axis cine CMR images. Two deep learning-based models in
spatial and frequency domains are proposed. Besides recognising these
artefacts, the proposed models are suitable to the common challenges of not
having access to data labels. An unsupervised domain adaptation method and a
Fourier-based convolutional neural network are proposed to overcome these
challenges. We show that the proposed models reliably allow for CMR image
quality assessment. The accuracies obtained for the spatial model in supervised
and weakly supervised learning are 99.41+0.24 and 96.37+0.66 for the UK Biobank
dataset, respectively. Using unsupervised domain adaptation can somewhat
overcome the challenge of not having access to the data labels. The maximum
achieved domain gap coverage in unsupervised domain adaptation is 16.86%.
Domain adaptation can significantly improve a 5-class classification task and
deal with considerable domain shift without data labels. Increasing the speed
of training and testing can be achieved with the proposed model in the
frequency domain. The frequency-domain model can achieve the same accuracy yet
1.548 times faster than the spatial model. This model can also be used directly
on k-space data, and there is no need for image reconstruction.Comment: 21 pages, 9 figures, 7 table
MRI Artefact Augmentation: Robust Deep Learning Systems and Automated Quality Control
Quality control (QC) of magnetic resonance imaging (MRI) is essential to establish whether a scan or dataset meets a required set of standards. In MRI, many potential artefacts must be identified so that problematic images can either be excluded or accounted for in further image processing or analysis. To date, the gold standard for the identification of these issues is visual inspection by experts.
A primary source of MRI artefacts is caused by patient movement, which can affect clinical diagnosis and impact the accuracy of Deep Learning systems. In this thesis, I present a method to simulate motion artefacts from artefact-free images to augment convolutional neural networks (CNNs), increasing training appearance variability and robustness to motion artefacts. I show that models trained with artefact augmentation generalise better and are more robust to real-world artefacts, with negligible cost to performance on clean data. I argue that it is often better to optimise frameworks end-to-end with artefact augmentation rather than learning to retrospectively remove artefacts, thus enforcing robustness to artefacts at the feature level representation of the data.
The labour-intensive and subjective nature of QC has increased interest in automated methods. To address this, I approach MRI quality estimation as the uncertainty in performing a downstream task, using probabilistic CNNs to predict segmentation uncertainty as a function of the input data. Extending this framework, I introduce a novel decoupled uncertainty model, enabling separate uncertainty predictions for different types of image degradation. Training with an extended k-space artefact augmentation pipeline, the model provides informative measures of uncertainty on problematic real-world scans classified by QC raters and enables sources of segmentation uncertainty to be identified.
Suitable quality for algorithmic processing may differ from an image's perceptual quality. Exploring this, I pose MRI visual quality assessment as an image restoration task. Using Bayesian CNNs to recover clean images from noisy data, I show that the uncertainty indicates the possible recoverability of an image. A multi-task network combining uncertainty-aware artefact recovery with tissue segmentation highlights the distinction between visual and algorithmic quality, which has the impact that, depending on the downstream task, less data should be discarded for purely visual quality reasons
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