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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2017)

The pathology of many cardiovascular diseases is believed to be heavily tied to local hemodynamics. A positive feedback loop of remodeling and unhealthy flow conditions can lead to blood vessel abnormalities, such as aneurysms, stenoses, and plaques. Doctors use medical imaging techniques to visualize vascular disease within patients. However, while treatments based on these images for some diseases have been well-established, there is room for improvement. Many treatment decisions are based on simplified criteria and incomplete data and our understanding behind the pathophysiology of many of these diseases remains woefully incomplete. A stronger grasp of the relationship between disease and hemodynamics can help clinicians plan better treatment outcomes or help prevent some complications from occurring.

4D-Magnetic Resonance (MR) Imaging can be a powerful tool for quantifying the flow field within the cardiovasculature, but remains difficult to integrate for clinical use due to the involving process required to convert noisy magnetic resonance image data from a set of symbols to an easily digestible image. Treatment decisions are based on standardized practices, but no standardization for the processing and interpretation of 4D-MR images exist. Computational Fluid Dynamics (CFD) can simulate patient hemodynamics with much finer temporal and spatial resolution than 4D-MR. However, computational methods must still use boundary conditions obtained from imaging data, which means CFD results can only be as accurate as the images they are based upon. Additionally, the logistics of performing CFD, which require extensive training and time, is a strong barrier against its adoption in a clinical setting.

This thesis presents a model for using in vivo (live) and simulated flow data as complementary methods to explore potential mechanisms of pathophysiology and aid the treatment of cardiovascular diseases. We developed pipelines for processing 4D-MR images and for building patient-specific CFD simulations. We first attempted to measure the experimental error in 4D-Flow MRI within a cerebral aneurysm phantom and explored how that error might propagate into CFD results based on those MR measurements. We used those results to predict how this sensitivity would affect the treatment of aneurysms based on their hemodynamics. We then used both 4D-MR and CFD methods to characterize a rarely explored vascular territory, the cerebral venous outflow tract (CVOT). 4D-Flow MR was used to categorize geometries and flows in the CVOT. CFD was used to investigate a potential association between flow and symptoms in a subcategory of internal jugular vein geometries.

    Cover page: Complementary 4D-Flow and CFD Analysis Methods for Investigating Pathological Hemodynamics
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2021)

    Objectives

    To determine the intra-individual flow variation in serially acquired studies, and the influence of this variation on subsequent hemodynamic simulations using the inlet flow as a boundary condition. Author: Kindly check and confirm whether the corresponding authors are correctly identified.Confirmed.

    Materials and methods

    This prospective study included 51 patients (37 females and 14 males) with unruptured intracranial aneurysms who have received more than three times follow-up of 2D phase-contrast MR. The flow and velocity parameters were extracted to calculate the reproducibility and variation. Patient-specific computational fluid dynamics simulations were performed using the measured flows.

    Results

    Intraclass correlation coefficients for mean and maximum velocity and flow parameters ranged from 0.77 to 0.90. A 10% CV of mean flow was identified. Variations of 10% in inlet flow resulted in hemodynamic changes including 41.41% of peak systolic wall shear stress; 39.13% of end-diastolic wall shear stress; 2.79% of low shear area at peak systole; 2.12% of low shear area at end diastole: 47.57% of time-averaged wall shear stress; and 0.17% of oscillatory shear index.

    Conclusion

    This study identified 10% of intra-individual mean flow variation on phase-contrast MR. Intra-individual flow variation resulted in a non-negligible variation in wall shear stress, but relatively small variation in low shear area in hemodynamic calculations.
      Cover page: Identification of intra-individual variation in intracranial arterial flow by MRI and the effect on computed hemodynamic descriptors
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2019)
      Intraluminal thrombus (ILT) is present in the majority of abdominal aortic aneurysms (AAA) of a size warranting consideration for surgical or endovascular intervention. The rupture risk of AAAs is thought to be related to the balance of vessel wall strength and the mechanical stress caused by systemic blood pressure. Previous finite element analyses of AAAs have shown that ILT can reduce and homogenize aneurysm wall stress. These works have largely considered ILT to be homogeneous in mechanical character or have idealized a stiffness distribution through the thrombus thickness. In this work, we use magnetic resonance imaging (MRI) to delineate the heterogeneous composition of ILT in 7 AAAs and perform patient-specific finite element analysis under multiple conditions of ILT layer stiffness disparity. We find that explicit incorporation of ILT heterogeneity in the finite element analysis is unlikely to substantially alter major stress analysis predictions regarding aneurysm rupture risk in comparison to models assuming a homogenous thrombus, provided that the maximal ILT stiffness is the same between models. Our results also show that under a homogeneous ILT assumption, the choice of ILT stiffness from values common in the literature can result in significantly larger variations in stress predictions compared to the effects of thrombus heterogeneity.
        Cover page: On the Relative Impact of Intraluminal Thrombus Heterogeneity on Abdominal Aortic Aneurysm Mechanics.
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2017)
        Pulsatile Tinnitus (PT) is a pulse-synchronous sound heard in the absence of an external source. PT is often related to abnormal flow in vascular structures near the cochlea. One vascular territory implicated in PT is the internal jugular vein (IJV). Using computational fluid dynamics (CFD) based on patient-specific Magnetic Resonance Imaging (MRI), we investigated the flow within the IJV of seven subjects, four symptomatic and three asymptomatic of PT. We found that there were two extreme anatomic types classified by the shape and position of the jugular bulbs: elevated and rounded. PT patients had elevated jugular bulbs that led to a distinctive helical flow pattern within the proximal internal jugular vein. Asymptomatic subjects generally had rounded jugular bulbs that neatly redirected flow from the sigmoid sinus directly into the jugular vein. These two flow patterns were quantified by calculating the length-averaged streamline curvature of the flow within the proximal jugular vein: 130.3±8.1m-1 for geometries with rounded bulbs, 260.7±29.4m-1 for those with elevated bulbs (P<0.005). Our results suggest that variations in the jugular bulb geometry lead to distinct flow patterns that are linked to PT, but further investigation is needed to determine if the vortex pattern is causal to sound generation.
          Cover page: Flow patterns in the jugular veins of pulsatile tinnitus patients
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2017)
          Segmentation of the geometric morphology of abdominal aortic aneurysm is important for interventional planning. However, the segmentation of both the lumen and the outer wall of aneurysm in magnetic resonance (MR) image remains challenging. This study proposes a registration based segmentation methodology for efficiently segmenting MR images of abdominal aortic aneurysms. The proposed methodology first registers the contrast enhanced MR angiography (CE-MRA) and black-blood MR images, and then uses the Hough transform and geometric active contours to extract the vessel lumen by delineating the inner vessel wall directly from the CE-MRA. The proposed registration based geometric active contour is applied to black-blood MR images to generate the outer wall contour. The inner and outer vessel wall are then fused presenting the complete vessel lumen and wall segmentation. The results obtained from 19 cases showed that the proposed registration based geometric active contour model was efficient and comparable to manual segmentation and provided a high segmentation accuracy with an average Dice value reaching 89.79%.
            Cover page: Segmentation of lumen and outer wall of abdominal aortic aneurysms from 3D black-blood MRI with a registration based geodesic active contour model
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2019)

            Purpose

            Segmentation of cardiac medical images, an important step in measuring cardiac function, is usually performed either manually or semiautomatically. Fully automatic segmentation of the left ventricle (LV), the right ventricle (RV) as well as the myocardium of three-dimensional (3D) magnetic resonance (MR) images throughout the entire cardiac cycle (four-dimensional, 4D), remains challenging. This study proposes a deformable-based segmentation methodology for efficiently segmenting 4D (3D + t) cardiac MR images.

            Methods

            The proposed methodology first used the Hough transform and the local Gaussian distribution method (LGD) to segment the LV endocardial contours from cardiac MR images. Following this, a novel level set-based shape prior method was applied to generate the LV epicardial contours and the RV boundary.

            Results

            This automatic image segmentation approach has been applied to studies on 17 subjects. The results demonstrated that the proposed method was efficient compared to manual segmentation, achieving a segmentation accuracy with average Dice values of 88.62 ± 5.47%, 87.35 ± 7.26%, and 82.63 ± 6.22% for the LV endocardial, LV epicardial, and RV contours, respectively.

            Conclusions

            We have presented a method for accurate LV and RV segmentation. Compared to three existing methods, the proposed method can successfully segment the LV and yield the highest Dice value. This makes it an option for clinical assessment of the volume, size, and thickness of the ventricles.
              Cover page: Fully automatic segmentation of 4D MRI for cardiac functional measurements
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2021)

              Background

              The segmentation of cardiac medical images is a crucial step for calculating clinical indices such as wall thickness, ventricular volume, and ejection fraction.

              Methods

              In this study, we introduce a method named LsUnet that combines multi-channel, fully convolutional neural network, and annular shape level-set methods for efficiently segmenting cardiac cine magnetic resonance (MR) images. In this method, the multi-channel deep learning algorithm is applied to train the segmentation task to extract the left ventricle (LV) endocardial and epicardial contours. Next, the segmentation contours from the multi-channel deep learning method are incorporated into a level-set formulation, which is dedicated explicitly to detecting annular shapes to assure the segmentation's accuracy and robustness.

              Results

              The proposed automatic approach was evaluated on 95 volumes (total 1,076 slices, ~80% as for training datasets, ~20% 2D as for testing datasets). This combined multi-channel deep learning and annular shape level-set segmentation method achieved high accuracy with average Dice values reaching 92.15% and 95.42% for LV endocardium and epicardium delineation, respectively, in comparison to the reference standard (the manual segmentation).

              Conclusions

              A novel method for fully automatic segmentation of the LV endocardium and epicardium from different MRI datasets is presented. The proposed workflow is accurate and robust compared to the reference and other state-of-the-art methods.
                Cover page: Deep learning based fully automatic segmentation of the left ventricular endocardium and epicardium from cardiac cine MRI
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2018)

                Objectives

                To evaluate an accelerated 4D flow MRI method that provides high temporal resolution in a clinically feasible acquisition time for intracranial velocity imaging.

                Materials and methods

                Accelerated 4D flow MRI was developed by using a pseudo-random variable-density Cartesian undersampling strategy (CIRCUS) with the combination of k-t, parallel imaging and compressed sensing image reconstruction techniques (k-t SPARSE-SENSE). Four-dimensional flow data were acquired on five healthy volunteers and eight patients with intracranial aneurysms using CIRCUS (acceleration factor of R = 4, termed CIRCUS4) and GRAPPA (R = 2, termed GRAPPA2) as the reference method. Images with three times higher temporal resolution (R = 12, CIRCUS12) were also reconstructed from the same acquisition as CIRCUS4. Qualitative and quantitative image assessment was performed on the images acquired with different methods, and complex flow patterns in the aneurysms were identified and compared.

                Results

                Four-dimensional flow MRI with CIRCUS was achieved in 5 min and allowed further improved temporal resolution of <30 ms. Volunteer studies showed similar qualitative and quantitative evaluation obtained with the proposed approach compared to the reference (overall image scores: GRAPPA2 3.2 ± 0.6; CIRCUS4 3.1 ± 0.7; CIRCUS12 3.3 ± 0.4; difference of the peak velocities: -3.83 ± 7.72 cm/s between CIRCUS4 and GRAPPA2, -1.72 ± 8.41 cm/s between CIRCUS12 and GRAPPA2). In patients with intracranial aneurysms, the higher temporal resolution improved capturing of the flow features in intracranial aneurysms (pathline visualization scores: GRAPPA2 2.2 ± 0.2; CIRCUS4 2.5 ± 0.5; CIRCUS12 2.7 ± 0.6).

                Conclusion

                The proposed rapid 4D flow MRI with a high temporal resolution is a promising tool for evaluating intracranial aneurysms in a clinically feasible acquisition time.
                  Cover page: Highly accelerated intracranial 4D flow MRI: evaluation of healthy volunteers and patients with intracranial aneurysms
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2020)

                  Hypothesis

                  We hypothesize patient-specific flow models to be an adequate in vitro surrogate to allow for characterization of pulsatile tinnitus (PT) that affects three to five million Americans.

                  Background

                  PT, rhythmic sounds without an extracorporeal source that patients appreciate, can be caused by aberrant blood flow in large cerebral veins near the cochlea. To investigate the sound production mechanism, we created 3D printed flow models based on patient-specific cerebral venous anatomies.

                  Methods

                  Magnetic resonance angiography datasets from two patients with PT were used to generate patient-specific 3D printed flow models. A flow circuit connecting the patient-specific models to a pulsatile, continuous flow pump simulating cardiac cycle was created. Sound recordings were made along the surface of the models using an electronic stethoscope. Peak-to-rms amplitude, and area under the power spectral density (PSD) curve values were computed to evaluate the sound measurements. Wilcoxon rank sum test was used to statistically determine the differences in measurements between the patient-specific models.

                  Results

                  In patient-1, the recordings (peak-to-rms) from the internal jugular vein stenosis of baseline model (4.29 ± 1.26 for 146 samples) were significantly louder (p < 0.001) than that of the altered model (3.29 ± 0.96 for 143 samples). In patient-2, the sound measured at the transverse sinus stenosis in the pre-lumbar puncture model (4.84 ± 1.11 for 148 samples) was significantly louder (p < 0.0001) than that of the post-lumbar puncture model (3.14 ± 0.87 for 135 samples).

                  Conclusions

                  The models are able to generate sounds very similar to those appreciated by patients and examiners in the cases of objective PT.
                    Cover page: Sound Measurement in Patient-Specific 3D Printed Bench Models of Venous Pulsatile Tinnitus.
                    • Article
                    Radiology (2020)

                    Idiopathic intracranial hypertension (IIH)

                    • Elevated intracranial pressure (ICP) with no clear cause

                    • Results in stenosed venous transverse sinus (TS)

                    •Stenosis causes pulsatile tinnitus

                    Treatment – Venous Sinus Stenting (VSS)

                    • Performed when the intravascular pressure (IVP) gradient across the stenosis is above 8 mmHg

                    • 10.3% revision surgery rate

                    • Most common reason for revision is the occurrence of a new stenosis upstream of the stent

                    • There is currently no standardized criteria for the selection of stents to be used in this procedure; they are used off-label

                      Cover page: Venous Sinus Stenosis Phantom
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