Development of multiparametric MRI models for prostate cancer detection based on improved correlative pathology

University of Minnesota Ph.D. dissertation. June 2014. Major: Biophysical Sciences and Medical Physics. Advisor: Gregory J. Metzger. 1 computer file (PDF); xix, 116 pages.Prostate cancer (PCa) is a prevalent disease which affects 1 in 6 men in the United States and has overtaken lung cancer as the leading cause of cancer related deaths in American men and number two worldwide. Among several diagnostic imaging tests that are available for detection of PCa in the market today, Magnetic Resonance Imaging (MRI) occupies a unique position in the detection of PCa due to its excellent soft tissue contrast and its ability to generate tissue property dependent multi-parametric data. While MRI has become an increasingly valuable tool in the management of men with PCa, its use to identify aggressive disease and characterize extent have yet to be developed. Multi-parametric MRI (MP-MRI) studies have been shown to increase sensitivity and specificity towards PCa detection compared to any single MRI dataset. The ability to develop and evaluate MP-MRI to prospectively detect disease, assess aggressiveness and delineate extent, first requires the retrospective validation against post-surgical pathology sections. Despite the large effort made by many groups in this area of research, the correlation of in vivo MP-MRI with pathology is still a challenge and to date is insufficient to develop highly accurate models of disease. To address this problem this thesis showcases (1) a novel registration approach called LATIS (Local Affine Transformation assisted by Internal Structures) for co-registering post prostatectomy pseudo-whole mount (PWM) pathological sections with in vivo MRI images and (2) MP-MRI based predictive model for disease detection using a composite biomarker score based on a unique database of pathology co-registered MR data sets. Also showcased in this thesis is a study where r1 and r2* relaxivities of a common paramagnetic contrast agent were measured in blood and saline at both 3T and 7T. This is important information to have when attempting to perform DCE-MRI studies as part of a MP-MRI protocol at ultra-high magnetic field strengths

3D fusion of histology to multi-parametric MRI for prostate cancer imaging evaluation and lesion-targeted treatment planning

Multi-parametric magnetic resonance imaging (mpMRI) of localized prostate cancer has the potential to support detection, staging and localization of tumors, as well as selection, delivery and monitoring of treatments. Delineating prostate cancer tumors on imaging could potentially further support the clinical workflow by enabling precise monitoring of tumor burden in active-surveillance patients, optimized targeting of image-guided biopsies, and targeted delivery of treatments to decrease morbidity and improve outcomes. Evaluating the performance of mpMRI for prostate cancer imaging and delineation ideally includes comparison to an accurately registered reference standard, such as prostatectomy histology, for the locations of tumor boundaries on mpMRI. There are key gaps in knowledge regarding how to accurately register histological reference standards to imaging, and consequently further gaps in knowledge regarding the suitability of mpMRI for tasks, such as tumor delineation, that require such reference standards for evaluation. To obtain an understanding of the magnitude of the mpMRI-histology registration problem, we quantified the position, orientation and deformation of whole-mount histology sections relative to the formalin-fixed tissue slices from which they were cut. We found that (1) modeling isotropic scaling accounted for the majority of the deformation with a further small but statistically significant improvement from modeling affine transformation, and (2) due to the depth (mean±standard deviation (SD) 1.1±0.4 mm) and orientation (mean±SD 1.5±0.9°) of the sectioning, the assumption that histology sections are cut from the front faces of tissue slices, common in previous approaches, introduced a mean error of 0.7 mm. To determine the potential consequences of seemingly small registration errors such as described above, we investigated the impact of registration accuracy on the statistical power of imaging validation studies using a co-registered spatial reference standard (e.g. histology images) by deriving novel statistical power formulae that incorporate registration error. We illustrated, through a case study modeled on a prostate cancer imaging trial at our centre, that submillimeter differences in registration error can have a substantial impact on the required sample sizes (and therefore also the study cost) for studies aiming to detect mpMRI signal differences due to 0.5 – 2.0 cm3 prostate tumors. With the aim of achieving highly accurate mpMRI-histology registrations without disrupting the clinical pathology workflow, we developed a three-stage method for accurately registering 2D whole-mount histology images to pre-prostatectomy mpMRI that allowed flexible placement of cuts during slicing for pathology and avoided the assumption that histology sections are cut from the front faces of tissue slices. The method comprised a 3D reconstruction of histology images, followed by 3D–3D ex vivo–in vivo and in vivo–in vivo image transformations. The 3D reconstruction method minimized fiducial registration error between cross-sections of non-disruptive histology- and ex-vivo-MRI-visible strand-shaped fiducials to reconstruct histology images into the coordinate system of an ex vivo MR image. We quantified the mean±standard deviation target registration error of the reconstruction to be 0.7±0.4 mm, based on the post-reconstruction misalignment of intrinsic landmark pairs. We also compared our fiducial-based reconstruction to an alternative reconstruction based on mutual-information-based registration, an established method for multi-modality registration. We found that the mean target registration error for the fiducial-based method (0.7 mm) was lower than that for the mutual-information-based method (1.2 mm), and that the mutual-information-based method was less robust to initialization error due to multiple sources of error, including the optimizer and the mutual information similarity metric. The second stage of the histology–mpMRI registration used interactively defined 3D–3D deformable thin-plate-spline transformations to align ex vivo to in vivo MR images to compensate for deformation due to endorectal MR coil positioning, surgical resection and formalin fixation. The third stage used interactively defined 3D–3D rigid or thin-plate-spline transformations to co-register in vivo mpMRI images to compensate for patient motion and image distortion. The combined mean registration error of the histology–mpMRI registration was quantified to be 2 mm using manually identified intrinsic landmark pairs. Our data set, comprising mpMRI, target volumes contoured by four observers and co-registered contoured and graded histology images, was used to quantify the positive predictive values and variability of observer scoring of lesions following the Prostate Imaging Reporting and Data System (PI-RADS) guidelines, the variability of target volume contouring, and appropriate expansion margins from target volumes to achieve coverage of histologically defined cancer. The analysis of lesion scoring showed that a PI-RADS overall cancer likelihood of 5, denoting “highly likely cancer”, had a positive predictive value of 85% for Gleason 7 cancer (and 93% for lesions with volumes \u3e0.5 cm3 measured on mpMRI) and that PI-RADS scores were positively correlated with histological grade (ρ=0.6). However, the analysis also showed interobserver differences in PI-RADS score of 0.6 to 1.2 (on a 5-point scale) and an agreement kappa value of only 0.30. The analysis of target volume contouring showed that target volume contours with suitable margins can achieve near-complete histological coverage for detected lesions, despite the presence of high interobserver spatial variability in target volumes. Prostate cancer imaging and delineation have the potential to support multiple stages in the management of localized prostate cancer. Targeted biopsy procedures with optimized targeting based on tumor delineation may help distinguish patients who need treatment from those who need active surveillance. Ongoing monitoring of tumor burden based on delineation in patients undergoing active surveillance may help identify those who need to progress to therapy early while the cancer is still curable. Preferentially targeting therapies at delineated target volumes may lower the morbidity associated with aggressive cancer treatment and improve outcomes in low-intermediate-risk patients. Measurements of the accuracy and variability of lesion scoring and target volume contouring on mpMRI will clarify its value in supporting these roles

Image-based registration methods for quantification and compensation of prostate motion during trans-rectal ultrasound (TRUS)-guided biopsy

Prostate biopsy is the clinical standard for cancer diagnosis and is typically performed under two-dimensional (2D) transrectal ultrasound (TRUS) for needle guidance. Unfortunately, most early stage prostate cancers are not visible on ultrasound and the procedure suffers from high false negative rates due to the lack of visible targets. Fusion of pre-biopsy MRI to 3D TRUS for targeted biopsy could improve cancer detection rates and volume of tumor sampled. In MRI-TRUS fusion biopsy systems, patient or prostate motion during the procedure causes misalignments in the MR targets mapped to the live 2D TRUS images, limiting the targeting accuracy of the biopsy system. In order to sample smallest clinically significant tumours of 0.5 cm3with 95% confidence, the root mean square (RMS) error of the biopsy system needs to be The target misalignments due to intermittent prostate motion during the procedure can be compensated by registering the live 2D TRUS images acquired during the biopsy procedure to the pre-acquired baseline 3D TRUS image. The registration must be performed both accurately and quickly in order to be useful during the clinical procedure. We developed an intensity-based 2D-3D rigid registration algorithm and validated it by calculating the target registration error (TRE) using manually identified fiducials within the prostate. We discuss two different approaches that can be used to improve the robustness of this registration to meet the clinical requirements. Firstly, we evaluated the impact of intra-procedural 3D TRUS imaging on motion compensation accuracy since the limited anatomical context available in live 2D TRUS images could limit the robustness of the 2D-3D registration. The results indicated that TRE improved when intra-procedural 3D TRUS images were used in registration, with larger improvements in the base and apex regions as compared with the mid-gland region. Secondly, we developed and evaluated a registration algorithm whose optimization is based on learned prostate motion characteristics. Compared to our initial approach, the updated optimization improved the robustness during 2D-3D registration by reducing the number of registrations with a TRE \u3e 5 mm from 9.2% to 1.2% with an overall RMS TRE of 2.3 mm. The methods developed in this work were intended to improve the needle targeting accuracy of 3D TRUS-guided biopsy systems. The successful integration of the techniques into current 3D TRUS-guided systems could improve the overall cancer detection rate during the biopsy and help to achieve earlier diagnosis and fewer repeat biopsy procedures in prostate cancer diagnosis

Factors Influencing Variability in the Performance of Multiparametric Magnetic Resonance Imaging in Detecting Clinically Significant Prostate Cancer: A Systematic Literature Review

CONTEXT: There is a lack of comprehensive data regarding the factors that influence the diagnostic accuracy of multiparametric magnetic resonance imaging (mpMRI) to detect and localize clinically significant prostate cancer (csPCa). OBJECTIVE: To systematically review the current literature assessing the factors influencing the variability of mpMRI performance in csPCa diagnosis. EVIDENCE ACQUISITION: A computerized bibliographic search of Medline/PubMed database was performed for all studies assessing magnetic field strength, use of an endorectal coil, assessment system used by radiologists and inter-reader variability, experience of radiologists and urologists, use of a contrast agent, and use of computer-aided diagnosis (CAD) tools in relation to mpMRI diagnostic accuracy. EVIDENCE SYNTHESIS: A total of 77 articles were included. Both radiologists' reading experience and urologists'/radiologists' biopsy experience were the main factors that influenced diagnostic accuracy. Therefore, it is mandatory to indicate the experience of the interpreting radiologists and biopsy-performing urologists to support the reliability of the findings. The most recent Prostate Imaging Reporting and Data System (PI-RADS) guidelines are recommended for use as the main assessment system for csPCa, given the simplified and standardized approach as well as its particular added value for less experienced radiologists. Biparametric MRI had similar accuracy to mpMRI; however, biparametric MRI performed better with experienced readers. The limited data available suggest that the combination of CAD and radiologist readings may influence diagnostic accuracy positively. CONCLUSIONS: Multiple factors affect the accuracy of mpMRI and MRI-targeted biopsy to detect and localize csPCa. The high heterogeneity across the studies underlines the need to define the experience of radiologists and urologists, implement quality control, and adhere to the most recent PI-RADS assessment guidelines. Further research is needed to clarify which factors impact the accuracy of the MRI pathway and how. PATIENT SUMMARY: We systematically reported the factors influencing the accuracy of multiparametric magnetic resonance imaging (mpMRI) in detecting clinically significant prostate cancer (csPCa). These factors are significantly related to each other, with the experience of the radiologists being the dominating factor. In order to deliver the benefits of mpMRI to diagnose csPCa, it is necessary to develop expertise for both radiologists and urologists, implement quality control, and adhere to the most recent Prostate Imaging Reporting and Data System assessment guidelines

The Role of Multiparametric MRI in Detection, Localization and Characterization of Prostate Cancer

Our aim was to detect the performance characteristics of multiparametric magnetic resonance imaging (mp-MRI) in patients with clinical suspicion, or previous diagnosis, of prostate cancer. Mp-MRI (index test) comprised of T2-weighted, diffusion weighted and dynamic contrast enhanced imaging. Radiologists used Likert score 1-5 based on the likelihood of the presence of prostate cancer. Concordance was made between results of mp- MRI and template prostate mapping (TPM) biopsy (reference standard). This retrospective study included patients that had both the index test and reference standard between January 2007 to January 2011 at either University College London Hospital or London Urology Associates.. These were patients with; a) no prior prostate biopsy (n=129), b) prior negative prostate biopsy (n=54), c) previous positive prostate biopsy (n=194) and d) biochemical failure after radiotherapy (n=37). A set of target conditions was used and varied between the four groups of patients. These were either based on Gleason scoring, maximum cancer core length or a combination of both. In the first group, mp-MRI showed encouraging diagnostic performance results in ruling out clinically significant prostate cancer with sensitivity and negative predictive value (NPV) up to 94% and 89%, respectively. Accuracy figures were similar in the second group with sensitivity and NPV reaching up to 90% and 95%, respectively. In patients that underwent mp-MRI before reclassification TPM biopsy (third group), NPV for predicting that cancer remained low risk (as detected on previous TRUS-guided biopsy) reached up to 100%. Positive predictive value for upgrade of prostate cancer disease on subsequent TPM biopsy reached up to 75% with diagnostic odds ratio up to 2.86. In the last group, a combination of T2-weighted + high b-value showed optimum mp-MRI performance. These results suggest that mp-MRI can be used as a triage test among different patient populations, to select patients that can avoid biopsy and those that need re-biopsy before entering an active surveillance program. Time and cost can be saved by using only certain MRI sequences in patients with biochemical failure after radiotherapy

Toward optimization of target planning for magnetic resonance image-targeted, 3D transrectal ultrasound-guided fusion prostate biopsy

The current clinical standard for diagnosis of prostate cancer (PCa) is 2D transrectal ultrasound (TRUS)-guided biopsy. However, this procedure has a false negative rate of 21-47% and therefore many patients return for repeat biopsies. A potential solution for improving upon this problem is “fusion” biopsy, where magnetic resonance imaging (MRI) is used for PCa detection and localization prior to biopsy. In this procedure, tumours are delineated on pre-procedural MRI and registered to the 3D TRUS needle guidance modality. However, fusion biopsy continues to yield false negative results and there remains a gap in knowledge regarding biopsy needle target selection. Within-tumour needle targets are currently chosen ad hoc by the operating clinician without accounting for guidance system and registration errors. The objective of this thesis was to investigate how the choice of target selection strategy and number of biopsy attempts made per lesion may affect PCa diagnosis in the presence of needle delivery error. A fusion prostate biopsy simulation software platform was developed, which allowed for the investigation of how needle delivery error affects PCa diagnosis and cancer burden estimation. Initial work was conducted using 3D lesions contoured on MRI by collaborating radiologists. The results indicated that more than one core must be taken from the majority of lesions to achieve a sampling probability 95% for a biopsy system with needle delivery error ≥ 3.5 mm. Furthermore, it was observed that the optimal targeting scheme depends on the relative levels of systematic and random needle delivery errors inherent to the specific fusion biopsy system. Lastly, PCa tumours contoured on digital histology images by genitourinary pathologists were used to conduct biopsy simulations. The results demonstrated that needle delivery error has a substantial impact on the biopsy core involvement observed, and that targeting of high-grade lesions may result in higher core involvement variability compared with lesions of all grades. This work represents a first step toward improving the manner in which lesions are targeted using fusion biopsy. Successful integration of these findings into current fusion biopsy system operation could lead to earlier PCa diagnosis with the need for fewer repeat biopsy procedures

Software and Hardware-based Tools for Improving Ultrasound Guided Prostate Brachytherapy

Minimally invasive procedures for prostate cancer diagnosis and treatment, including biopsy and brachytherapy, rely on medical imaging such as two-dimensional (2D) and three-dimensional (3D) transrectal ultrasound (TRUS) and magnetic resonance imaging (MRI) for critical tasks such as target definition and diagnosis, treatment guidance, and treatment planning. Use of these imaging modalities introduces challenges including time-consuming manual prostate segmentation, poor needle tip visualization, and variable MR-US cognitive fusion. The objective of this thesis was to develop, validate, and implement software- and hardware-based tools specifically designed for minimally invasive prostate cancer procedures to overcome these challenges. First, a deep learning-based automatic 3D TRUS prostate segmentation algorithm was developed and evaluated using a diverse dataset of clinical images acquired during prostate biopsy and brachytherapy procedures. The algorithm significantly outperformed state-of-the-art fully 3D CNNs trained using the same dataset while a segmentation time of 0.62 s demonstrated a significant reduction compared to manual segmentation. Next, the impact of dataset size, image quality, and image type on segmentation performance using this algorithm was examined. Using smaller training datasets, segmentation accuracy was shown to plateau with as little as 1000 training images, supporting the use of deep learning approaches even when data is scarce. The development of an image quality grading scale specific to 3D TRUS images will allow for easier comparison between algorithms trained using different datasets. Third, a power Doppler (PD) US-based needle tip localization method was developed and validated in both phantom and clinical cases, demonstrating reduced tip error and variation for obstructed needles compared to conventional US. Finally, a surface-based MRI-3D TRUS deformable image registration algorithm was developed and implemented clinically, demonstrating improved registration accuracy compared to manual rigid registration and reduced variation compared to the current clinical standard of physician cognitive fusion. These generalizable and easy-to-implement tools have the potential to improve workflow efficiency and accuracy for minimally invasive prostate procedures

Automatic analysis of medical images for change detection in prostate cancer

Prostate cancer is the most common cancer and second most common cause of cancer death in men in the UK. However, the patient risk from the cancer can vary considerably, and the widespread use of prostate-specific antigen (PSA) screening has led to over-diagnosis and over-treatment of low-grade tumours. It is therefore important to be able to differentiate high-grade prostate cancer from the slowly- growing, low-grade cancer. Many of these men with low-grade cancer are placed on active surveillance (AS), which involves constant monitoring and intervention for risk reclassification, relying increasingly on magnetic resonance imaging (MRI) to detect disease progression, in addition to TRUS-guided biopsies which are the routine clinical standard method to use. This results in a need for new tools to process these images. For this purpose, it is important to have a good TRUS-MR registration so corresponding anatomy can be located accurately between the two. Automatic segmentation of the prostate gland on both modalities reduces some of the challenges of the registration, such as patient motion, tissue deformation, and the time of the procedure. This thesis focuses on the use of deep learning methods, specifically convolutional neural networks (CNNs), for prostate cancer management. Chapters 4 and 5 investigated the use of CNNs for both TRUS and MRI prostate gland segmentation, and reported high segmentation accuracies for both, Dice Score Coefficients (DSC) of 0.89 for TRUS segmentations and DSCs between 0.84-0.89 for MRI prostate gland segmentation using a range of networks. Chapter 5 also investigated the impact of these segmentation scores on more clinically relevant measures, such as MRI-TRUS registration errors and volume measures, showing that a statistically significant difference in DSCs did not lead to a statistically significant difference in the clinical measures using these segmentations. The potential of these algorithms in commercial and clinical systems are summarised and the use of the MRI prostate gland segmentation in the application of radiological prostate cancer progression prediction for AS patients are investigated and discussed in Chapter 8, which shows statistically significant improvements in accuracy when using spatial priors in the form of prostate segmentations (0.63 ± 0.16 vs. 0.82 ± 0.18 when comparing whole prostate MRI vs. only prostate gland region, respectively)