Purang Abolmaesumi

Professor

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Biography

Purang Abolmaesumi received his BSc (1995) and MSc (1997) from Sharif University of Technology, Iran, and his PhD (2002) from UBC, all in electrical engineering. From 2002 to 2009, he was a faculty member with the School of Computing, Queen’s University. He then joined the Department of Electrical and Computer Engineering at UBC, where he is a Canada Research Chair, Tier II, in Biomedical Engineering and a Professor, with Associate Membership to the Department of Urologic Sciences.

Dr. Abolmaesumi is internationally recognized and has received numerous awards for his pioneering developments in ultrasound image processing, image registration and image-guided interventions. He is the recepient of the Killam Faculty Research Prize at UBC. He currently serves as an Associate Editor of the IEEE Transactions on Medical Imaging, and has served as an Associate Editor of the IEEE TBME between 2008 and 2012. He is a Board Member of the International Society for Computer Aided Surgery, and serves on the Program Committees of the Medical Image Computing and Computing and Computer Assisted Intervention (MICCAI), International Society for Optics and Photonics (SPIE) Medical Imaging, and the International Conference on Information Processing in Computer Assisted Interventions (IPCAI). Dr. Abolmaesumi is the General Chair of IPCAI 2014 and 2015, and has served as Program Chair of IPCAI 2012 in Pisa and Workshop and Tutorial Chair of MICCAI 2011 in Toronto.

Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - Mar 2019)
Overcoming obstacles in biomechanical modelling : methods for dealing with discretization, data fusion, and detail (2019)

Biomechanical modelling has the potential to start the next revolution in medicine, just as imaging has done in decades past. Current technology can now capture extremely detailed information about the structure of the human body. The next step is to consider function. Unfortunately, though there have been recent advances in creating useful anatomical models, there are still significant barriers preventing their widespread use.In this work, we aim to address some of the major challenges in biomechanical model construction. We examine issues of discretization: methods for representing complex soft tissue structures; issues related to consolidation of data: how to register information from multiple sources, particularly when some aspects are unreliable; and issues of detail: how to incorporate information necessary for reproducing function while balancing computational efficiency.To tackle discretization, we develop a novel hex-dominant meshing approach that allows for quality control. Our pattern-base tetrahedral recombination algorithm is extremely simple, and has tight computational bounds. We also compare a set of non-traditional alternatives in the context of muscle simulation to determine when each might be appropriate for a given application.For the fusion of data, we introduce a dynamics-driven registration technique which is robust to noise and unreliable information. It allows us to encode both physical and statistical priors, which we show can reduce error compared to the existing methods. We apply this to image registration for prostate interventions, where only parts of the anatomy are visible in images, as well as in creating a subject-specific model of the arm, where we need to adjust for both changes in shape and in pose.Finally, we examine the importance of and methods to include architectural details in a model, such as muscle fibre distribution, the stiffness of thin tendinous structures, and missing surface information. We examine the simulation of muscle contractions in the forearm, force transmission in the masseter, and dynamic motion in the upper airway to support swallowing and speech simulations.By overcoming some of these obstacles in biomechanical modelling, we hope to make it more accessible and practical for both research and clinical use.

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A machine learning framework for temporal enhanced ultrasound guided prostate cancer diagnostics (2018)

The ultimate diagnosis of prostate cancer involves histopathology analysis of tissue samples obtained through prostate biopsy, guided by either transrectal ultrasound (TRUS), or fusion of TRUS with multi-parametric magnetic resonance imaging. Appropriate clinical management of prostate cancer requires accurate detection and assessment of the grade of the disease and its extent. Despite recent advancements in prostate cancer diagnosis, accurate characterization of aggressive lesions from indolent ones is an open problem and requires refinement.Temporal Enhanced Ultrasound (TeUS) has been proposed as a new paradigm for tissue characterization. TeUS involves analysis of a sequence of ultrasound radio frequency (RF) or Brightness (B)-mode data using a machine learning approach. The overarching objective of this dissertation is to improve the accuracy of detecting prostate cancer, specifically the aggressive forms of the disease and to develop a TeUS-augmented prostate biopsy system. Towards full-filling this objective, this dissertation makes the following contributions: 1) Several machine learning techniques are developed and evaluated to automatically analyze the spectral and temporal aspect of backscattered ultrasound signals from the prostate tissue, and to detect the presence of cancer; 2) a patient-specific biopsy targeting approach is proposed that displays near real-time cancer likelihood maps on B-mode ultrasound images augmenting their information; and 3) the latent representations of TeUS, as learned by the proposed machine learning models, are investigated to derive insights about tissue dependent features residing in TeUS and their physical interpretation.A data set consisting of biopsy targets in mp-MRI-TRUS fusion-biopsies with 255 biopsy cores from 157 subjects was used to generate and evaluate the proposed techniques. Clinical histopathology of the biopsy cores was used as the gold-standard. Results demonstrated that TeUS is effective in differentiating aggressive prostate from clinically less-significant disease and non-cancerous tissue. Evidence derived from simulation and latent-feature visualization showed that micro-vibrations of tissue microstructure, captured by low-frequency spectral features of TeUS, is a main source of tissue-specific information that can be used for detection of prostate cancer.

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Adaptive ultrasound imaging to improve the visualization of spine and associated structures (2018)

Visualizing vertebrae or other bone structures clearly in ultrasound imaging is important for many clinical applications such as ultrasound-guided spinal needle injections and scoliosis detection. Another growing research topic is fusing ultrasound with other imaging modalities to get the benefit from each modality. In such approaches, tissue with strong interfaces, such as bones, are typically extracted and used as the feature for registration. Among those applications, the spine is of particular interest in this thesis. Although such ultrasound applications are promising, clear visualization of spine structures in ultrasound imaging is difficult due to factors such as specular reflection, off-axis energy and reverberation artifacts. The received channel ultrasound data from the spine are often tilted even after delay correction, resulting in signal cancellation during the beamforming process. Conventional beamformers are not designed to tackle this issue. In this thesis, we propose three beamforming methods dedicated to improve the visualization of spine structures. These methods include an adaptive beamforming method which utilizes the accumulated phase change across the receive aperture as the beamforming weight. Then, we propose a log-Gabor based directional filtering method to regulate the tilted channel data back to the beamforming direction to avoid bone signal cancellation. Finally, we present a closed-loop beamforming method which feeds back the location of the spine to the beamforming process so that backscattered bone signals can be aligned prior-to the beamforming. Field II simulation, phantom and in vivo results confirm significant contrast improvement of spinal structures compared with the conventional delay-and-sum beamforming and other adaptive beamforming methods.

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Registration of preoperative CT to intraoperative ultrasound via a statistical wrist model for scaphoid fracture fixation (2017)

Scaphoid fracture is the most probable outcome of wrist injury and it often occurs due to sudden fall on an outstretched arm. To fix an acute non-displaced fracture, a volar percutaneous surgical procedure is highly recommended as it provides faster healing and better biomechanical outcome to the recovered wrist. Conventionally, this surgical procedure is performed under X-ray based fluoroscopic guidance, where surgeons need to mentally determine a trajectory of the drilling path based on a series of 2D projection images. In addition to challenges associated with mapping 2D information to a 3D space, the process involves exposure to ionizing radiation. Ultrasound (US) has been suggested as an alternate; US has many advantages including its non-ionizing nature and real-time 3D acquisition capability. US images are, however, difficult to interpret as they are often corrupted by significant amounts of noise or artifact, in addition, the appearance of the bone surfaces in an US image contains only a limited view of the true surfaces. In this thesis, I propose techniques to enable ultrasound guidance in scaphoid fracture fixation by augmenting intraoperative US images with preoperative computed tomography (CT) images via a statistical anatomical model of the wrist. One of the major contributions is the development of a multi-object statistical wrist shape+scale+pose model from a group of subjects at wide range of wrist positions. The developed model is then used to register with the preoperative CT to obtain the shapes and sizes of the wrist bones. The intraoperative procedure starts with a novel US bone enhancement technique that takes advantage of an adaptive wavelet filter bank to accurately highlight the bone responses in US. The improved bone enhancement in turn enables a registration of the statistical pose model to intraoperative US to estimate the optimal scaphoid screw axis for guiding the surgical procedure. In addition to this sequential registration technique, I propose a joint registration technique that allows a simultaneous fusion of the US and CT data for an improved registration output. We conduct a cadaver experiment to determine the accuracy of the registration process, and compare the results with the ground truth.

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Information fusion for prostate brachytherapy planning (2016)

Low-dose-rate prostate brachytherapy is a minimally invasive treatment approach for localized prostate cancer. It takes place in one session by permanent implantation of several small radio-active seeds inside and adjacent to the prostate. The current procedure at the majority of institutions requires planning of seed locations prior to implantation from transrectal ultrasound (TRUS) images acquired weeks in advance. The planning is based on a set of contours representing the clinical target volume (CTV). Seeds are manually placed with respect to a planning target volume (PTV), which is an anisotropic dilation of the CTV, followed by dosimetry analysis. The main objective of the plan is to meet clinical guidelines in terms of recommended dosimetry by covering the entire PTV with the placement of seeds. The current planning process is manual, hence highly subjective, and can potentially contribute to the rate and type of treatment related morbidity. The goal of this thesis is to reduce subjectivity in prostate brachytherapy planning. To this end, we developed and evaluated several frameworks to automate various components of the current prostate brachytherapy planning process. This involved development of techniques with which target volume labels can be automatically delineated from TRUS images. A seed arrangement planning approach was developed by distributing seeds with respect to priors and optimizing the arrangement according to the clinical guidelines. The design of the proposed frameworks involved the introduction and assessment of data fusion techniques that aim to extract joint information in retrospective clinical plans, containing the TRUS volume, the CTV, the PTV and the seed arrangement. We evaluated the proposed techniques using data obtained in a cohort of 590 brachytherapy treatment cases from the Vancouver Cancer Centre, and compare the automation results with the clinical gold-standards and previously delivered plans. Our results demonstrate that data fusion techniques have the potential to enable automatic planning of prostate brachytherapy.

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Image-based guidance for prostate interventions (2015)

Prostate biopsy is the gold standard for cancer diagnosis. This procedure is guided using a 2D transrectal ultrasound (TRUS) probe. Unfortunately, early stage tumors are not visible in ultrasound and prostate motion/deformations make targeting challenging. This results in a high number of false negatives and patients are often required to repeat the procedure. Fusion of magnetic resonance images (MRI) into the workspace of a prostate biopsy has the potential to detect tumors invisible in TRUS. This allows the radiologist to better target early stage cancerous lesions. However, due to different body positions and imaging settings, the prostate undergoes motion and deformation between the biopsy coordinate system and the MRI. Furthermore, due to variable probe pressure, the prostate moves and deforms during biopsy as well. This introduces additional targeting errors. A biopsy system that compensates for these sources of error has the potential to improve the targeting accuracy and maintain a 3D record of biopsy locations. The goal of this thesis is to provide the necessary tools to perform freehand MR-TRUS fusion for prostate biopsy using a 3D guidance system. To this end, we have developed two novel surface-based registration methods for incorporating the MRI into the biopsy workspace. The proposed methods are the first methods that are robust to missing surface regions for MR-TRUS fusion (up to 30% missing surface points). We have validated these fusion techniques on 19 biopsy, 10 prostatectomy and 11 brachytherapy patients. In this thesis, we have also developed methods that combine intensitybased information with biomechanical constraints to compensate for prostate motion and deformations during the biopsy. To this end, we have developed a novel 2D-3D registration framework, which was validated on an additional 10 biopsy patients. Our results suggest that accurate 2D-3D registration for freehand biopsy is feasible.The results presented suggest that accurate registration of MR and TRUS data in the presence of partially missing data is feasible. Moreover, we demonstrate that in the presence of variable probe pressure during freehand biopsy, a combination of intensity-based and biomechanically constrained 2D-3D registration can enable accurate alignment of pre-procedure TRUS with 2D real time TRUS images.

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Joint source based brain imaging analysis for classification of individuals (2015)

Diagnosis and clinical management of neurological disorders that affect brain structure, function and networks would benefit substantially from the development of techniques that combine multi-modal and/or multi-task information. Here, we propose a joint Source Based Analysis (jSBA) framework to identify common information across structural and functional contrasts in data from MRI and fMRI experiments, for classification of individuals with neurological and psychiatric disorders. The framework consists of three components: 1) individual's feature generation, 2) joint group analysis, and 3) classification of individuals based on the group's generated features. In the proposed framework, information from brain neuroimaging datasets is reduced to a feature that is a lower-dimensional representation of a selected brain structure or task-related activation pattern. For each individual, features are used within a joint analysis method to generate basis brain activation sources and their corresponding modulation profiles. Modulation profiles are used to classify individuals into different categories. We perform two experiments to demonstrate the potential of the proposed framework to classify groups of subjects based on structural and functional brain data. In the fMRI analysis, functional contrast images derived from a study of auditory and speech perception of 16 young and 16 older adults are used for classification of individuals. First, we investigate the effect of using multi-task fMRI data to improve the classification accuracy. Then, we propose a novel joint Sparse Representation Analysis (jSRA) to identify common information across different functional contrasts in data. We further assess the reliability of jSRA, and visualize the brain patterns obtained from such analysis. In the sMRI analysis, features representing position, orientation and size (i.e. pose), shape, and local tissue composition of brain are used to classify 19 depressed and 26 healthy individuals. First, we incorporate pose and shape measures of morphology, which are not usually analyzed in neuromorphometric studies, to measure structural changes. Then, we combine brain tissue composition and morphometry using the proposed jSBA framework. In a cross-validation leave-one-out experiment, we show that we can classify the subjects with an accuracy of 67% solely based on the information gathered from the joint analysis of features obtained from multiple brain structures.

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New methods for calibration and tool tracking in ultrasound-guided interventions (2015)

Ultrasound is a safe, portable, inexpensive and real-time modality that can produce 2D and 3D images. It is a valuable intra-operative imaging modality to guide surgeons aiming to achieve higher accuracy of the intervention and improve patient outcomes. In all the clinical applications that use tracked ultrasound, one main challenge is to precisely locate the ultrasound image pixels with respect to a tracking sensor on the transducer. This process is called spatial calibration and the objective is to determine the spatial transformation between the ultrasound image coordinates and a coordinate system defined by the tracking sensor on the transducer housing. Another issue in ultrasound guided interventions is that tracking surgical tools (for example an epidural needle) usually requires expensive, large optical trackers or low accuracy magnetic trackers and there is a need for a low-cost, easy-to-use and accurate solution. In this thesis, for the first problem I have proposed two novel complementary methods for ultrasound calibration that provide ease of use and high accuracy. These methods are based on my differential technique which enables high measurement accuracy. I developed a closed-form formulation that makes it possible to achieve high accuracy with using a low number of images. For the second problem, I developed a method to track surgical tools (epidural needles in particular) using a single camera mounted on the ultrasound transducer to facilitate ultrasound guided interventions. The first proposed ultrasound calibration method achieved an accuracy of 0.09 ± 0.39 mm. The second method with a much simpler phantom yet achieved similar accuracy compared to the N-wire method. The proposed needle tracking method showed high accuracy of 0.94 ± 0.46 mm.

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Speckle tracking for 3D freehand ultrasound reconstruction (2014)

The idea of full six degree-of-freedom tracking of ultrasound images solely based on speckle information has been a long term research goal. It would eliminate the need for any additional tracking hardware and reduces cost and complexity of ultrasound imaging system, while providing the benefits of three-dimensional imaging.Despite its significant promise, speckle tracking has proven challenging due to several reasons including the dependency on a rare kind of speckle pattern in real tissue, underestimation in the presence of coherency or specular reflection, ultrasound beam profile spatial variations, need for RF (Radio Frequency) data, and artifacts produced by out-of-plane rotation. So, there is a need to improve the utility of freehand ultrasound in clinics by developing techniques to tackle these challenges and evaluate the applicability of the proposed methods for clinical use.We introduce a model-fitting method of speckle tracking based on the Rician Inverse Gaussian (RiIG) distribution. We derive a closed-form solution of the correlation coefficient of such a model, necessary for speckle tracking. In this manner, it is possible to separate the effect of the coherent and the non-coherent part of each patch. We show that this will increase the accuracy of the out-of-plane motion estimation.We also propose a regression-based model to compensate for the spatial changes of the beam profile.Although RiIG model fitting increases the accuracy, it is only applicable on ultrasound sampled RF data and computationally expensive. We propose a new framework to extract speckle/noise directly from B-mode images and perform speckle tracking on the extracted noise. To this end, we investigate and develop Non-Local Means (NLM) denoising algorithm based on a prior noise formation model.Finally, in order to increase the accuracy of the 6-DoF transform estimation, we propose a new iterative NLM denoising filter for the previously introduced RiIG model based on a new NLM similarity measure definition. The local estimation of the displacements are aggregated using Stein’s Unbiased Risk Estimate (SURE) over the entire image. The proposed filter-based speckle tracking algorithm has been evaluated in a set of ex vivo and in vivo experiments.

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Statistical models of the spine for image analysis and image-guided interventions (2014)

The blind placement of an epidural needle is among the most difficult regional anesthetic techniques. The challenge is to insert the needle in the midline plane of the spine and to avoid overshooting the needle into the spinal cord. Prepuncture 2D ultrasound scanning has been introduced as a reliable tool to localize the target and facilitate epidural needle placement. Ideally, real-time ultrasound should be used during needle insertion to monitor the progress of needle towards the target epidural space. However, several issues inhibit the use of standard 2D ultrasound, including the obstruction of the puncture site by the ultrasound probe, low visibility of the target in ultrasound images of the midline plane, and increased pain due to a longer needle trajectory. An alternative is to use 3D ultrasound imaging, where the needle and target could be visible within the same reslice of a 3D volume; however, novice ultrasound users (i.e., many anesthesiologists) have difficulty interpreting ultrasound images of the spine and identifying the target epidural space. In this thesis, I propose techniques that are utilized for augmentation of 3D ultrasound images with a model of the vertebral column. Such models can be pre-operatively generated by extracting the vertebrae from various imaging modalities such as Computed Tomography (CT) or Magnetic Resonance Imaging (MRI). However, these images may not be obtainable (such as in obstetrics), or involve ionizing radiation. Hence, the use of Statistical Shape Models (SSM) of the vertebrae is a reasonable alternative to pre-operative images. My techniques include construction of a statistical model of vertebrae and its registration to ultrasound images. The model is validated against CT images of 56 patients by evaluating the registration accuracy. The feasibility of the model is also demonstrated via registration to 64 in vivo ultrasound volumes.

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Master's Student Supervision (2010-2017)
Joint multimodal registration of medical images to a statistical model of the lumbar spine for spine anesthesia (2016)

Facet joint injections and epidural needle insertions are widely used for spine anesthesia. Needle guidance is usually performed by fluoroscopy or palpation, resulting in radiation exposure and multiple needle re-insertions. Several ultrasound (US)-based guidance approaches have been proposed to eliminate such issues.However, but they have not widely accepted in clinics due to difficulties in interpretation of the complex spinal anatomy in US, which leads to clinicians' lack of confidence in relying only on information derived from US for needle guidance.In this thesis, a model-based multi-modal joint registration framework is introduced, where a statistical model of the lumbar spine is concurrently registered to intraprocedure US and easy-to-interpret preprocedure images. The goal is to take advantage of the complementary features visible in US and preprocedure images, namely Computed Topography (CT) and Magnetic Resonance (MR) scans. Two versions of a lumbar spine statistical model are employed: a shape+pose model and a shape+pose+scale model. The underlying assumption is that the shape and size of the spine of a given subject are common amongst all imaging modalities . However, the pose of the spine changes from one modality to another, as the patient's position is different at different image acquisitions. The proposed method has been successfully validated on two datasets: (i) 10 pairs of US and CT scans and (ii) nine US and MR images of the lumbar spine. Using the shape+pose+scale model on the US+CT dataset, mean surface distance error of 2.42 mm for CT and mean Target Registration Error (TRE) of 3.14 mm for US were achieved. As for the US+MR dataset, TRE of 2.62 mm and 4.20 mm for the MR and US images, respectively. Both models models were equally accurate on the US+CT dataset. For US+MR, the shape+pose+scale model outperformed the shape+pose model. The joint registration allows augmentation of important anatomical landmarks in both intraprocedure US and preprocedure domains. Furthermore, observing the patient-specific model in preprocedure domains allows the clinicians to assess the local registration accuracy qualitatively. This can increase their confidence in using the US model for deriving needle guidance decisions.

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Simultaneous analysis of 2D echo views for left atrial segmentation and disease quantification (2016)

We propose a joint information framework for automatic analysis of 2D echocardiography (echo) data. The analysis combines a priori images, their segmentations and patient diagnostic information within a unified framework to determine various clinical parameters, such as cardiac chamber volumes, and cardiac disease labels. The main idea behind the framework is to employ joint Independent Component Analysis of both echo image intensity information and corresponding segmentation labels to generate models that jointly describe the image and label space of echo patients on multiple apical views jointly, instead of independently. These models are then both used for segmentation and volume estimation of cardiac chambers such as the left atrium and for detecting pathological abnormalities such as mitral regurgitation. We validate the approach on a large cohort of echos obtained from 6,993 studies. We report performance of the proposed framework in estimation of the left-atrium volume and diagnosis of mitral-regurgitation severity. A correlation coefficient of 0.87 was achieved for volume estimation of the left atrium when compared to the clinical report. Moreover, we classified patients that suffer from moderate or severe mitral regurgitation diagnosis with an average accuracy of 82%. Using only B-Mode echo information to automatically derive these clinical parameters, there is potential for this approach to be used clinically.

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Automatic vertebrae localization, identification, and segmentation using deep learning and statistical models (2014)

Automatic localization and identification of vertebrae in medical images of the spine are core requirements for building computer-aided systems for spine diagnosis. Automated algorithms for segmentation of vertebral structures can also benefit these systems for diagnosis of a range of spine pathologies. The fundamental challenges associated with the above-stated tasks arise from the repetitive nature of vertebral structures, restrictions in field of view, presence of spine pathologies or surgical implants, and poor contrast of the target structures in some imaging modalities. This thesis presents an automatic method for localization, identification, and segmentation of vertebrae in volumetric computed tomography (CT) scans and magnetic resonance (MR) images of the spine. The method makes no assumptions about which section of the vertebral column is visible in the image. An efficient deep learning approach is used to predict the location of each vertebra based on its contextual information in the image. Then, a statistical multi-vertebrae model is initialized by the localized vertebrae from the previous step. An iterative expectation maximization technique is used to register the statistical multi-vertebrae model to the edge points of the image in order to achieve a fast and reliable segmentation of vertebral bodies. State-of-the-art results are obtained for vertebrae localization in a public dataset of 224 arbitrary-field-of-view CT scans of pathological cases. Promising results are also obtained from quantitative evaluation of the automated segmentation method on volumetric MR images of the spine.

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Feature-based registration of preoperative CT to intraoperative 3-D ultrasound in laparoscopic partial nephrectomy using a priori CT segmentation (2011)

Robotic laparoscopic partial nephrectomy is a state-of-the-art procedure for the excision of renal tumours. The challenges of this surgery along with the stereoscopic interface to the surgeon make it an ideal candidate for image guidance. We propose bringing pre-operative computed tomography data to the patient's coordinate system using three-dimensional intraoperative back ultrasound. Since computed tomography and ultrasound images represent like anatomical information quite differently, we perform a manual segmentation of the computed tomography before the operation and a semi-automatic segmentation of the ultrasound intra-operatively. The segmentation of the kidney boundary facilitates a feature-based registration strategy.Semi-automatic segmentation of kidney ultrasound images is difficult because the edges with large gradient values do not correspond to the capsule boundary seen in computed tomography. The desired edges are actually quite faint in ultrasound and poorly detected by common edge methods such as the Canny approach.After trying a number of approaches, the best results were obtained using a novel interacting multiple-model probabilistic data association filter to select edges from ultrasound images that were filtered for phase congruency. The manual segmentation of the prior is used to guide edge detection in ultrasound. Experiments on seven pre-operative patient datasets and one intra-operative patient dataset resulted in a mean volume error ratio of 0.80 +/- 0.13 from after registration to before registration. These results came after the implementation and evaluation of numerous other approaches, including radial edge filters, the covariance matrix adaptation evolution strategy, and a deformable approach using geodesic active contours.The main contribution of this work is a method for the registration of the pre-operative planning data from computerized tomography to the intraoperative ultrasound. For clinical use, this method requires some form of calibration with the laparoscopic camera and integration with surgical visualization tools. Through integration with emerging technologies, the approach presented here can one day augment the surgical field-of-view and guide the surgeon around important anatomical structures to the tissue that must be excised.

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