Robert Toth

Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge

Prostate MRI image segmentation has been an area of intense research due to the increased use of MRI as a modality for the clinical workup of prostate cancer. Segmentation is useful for various tasks, e.g. to accurately localize prostate boundaries for radiotherapy or to initialize multi-modal registration algorithms. In the past, it has been difficult for research groups to evaluate prostate segmentation algorithms on multi-center, multi-vendor and multi-protocol data. Especially because we are dealing with MR images, image appearance, resolution and the presence of artifacts are affected by differences in scanners and/or protocols, which in turn can have a large influence on algorithm accuracy. The Prostate MR Image Segmentation (PROMISE12) challenge was setup to allow a fair and meaningful comparison of segmentation methods on the basis of performance and robustness. In this work we will discuss the initial results of the online PROMISE12 challenge, and the results obtained in the live challenge workshop hosted by the MICCAI2012 conference. In the challenge, 100 prostate MR cases from 4 different centers were included, with differences in scanner manufacturer, field strength and protocol. A total of 11 teams from academic research groups and industry participated. Algorithms showed a wide variety in methods and implementation, including active appearance models, atlas registration and level sets. Evaluation was performed using boundary and volume based metrics which were combined into a single score relating the metrics to human expert performance. The winners of the challenge where the algorithms by teams Imorphics and ScrAutoProstate, with scores of 85.72 and 84.29 overall. Both algorithms where significantly better than all other algorithms in the challenge (p<0.05) and had an efficient implementation with a run time of 8min and 3s per case respectively. Overall, active appearance model based approaches seemed to outperform other approaches like multi-atlas registration, both on accuracy and computation time. Although average algorithm performance was good to excellent and the Imorphics algorithm outperformed the second observer on average, we showed that algorithm combination might lead to further improvement, indicating that optimal performance for prostate segmentation is not yet obtained. All results are available online at http://promise12.grand-challenge.org/.

Central gland and peripheral zone prostate tumors have significantly different quantitative imaging signatures on 3 tesla endorectal, in vivo T2-weighted MR imagery

To identify and evaluate textural quantitative imaging signatures (QISes) for tumors occurring within the central gland (CG) and peripheral zone (PZ) of the prostate, respectively, as seen on in vivo 3 Tesla (T) endorectal T2‐weighted (T2w) MRI.

Multifeature Landmark-Free Active Appearance Models: Application to Prostate MRI Segmentation

Active shape models (ASMs) and active appearance models (AAMs) are popular approaches for medical image segmentation that use shape information to drive the segmentation process. Both approaches rely on image derived landmarks (specified either manually or automatically) to define the objects shape, which require accurate triangulation and alignment. An alternative approach to modeling shape is the level-set representation, defined as a set of signed distances to the objects surface. In addition, using multiple image derived attributes (IDAs) such as gradient information has previously shown to offer improved segmentation results when applied to ASMs, yet little work has been done exploring IDAs in the context of AAMs. In this work, we present a novel AAM methodology that utilizes the level set implementation to overcome the issues relating to specifying landmarks, and locates the object of interest in a new image using a registration based scheme. Additionally, the framework allows for incorporation of multiple IDAs. Our multifeature landmark-free AAM (MFLAAM) utilizes an efficient, intuitive, and accurate algorithm for identifying those IDAs that will offer the most accurate segmentations. In this paper, we evaluate our MFLAAM scheme for the problem of prostate segmentation from T2-w MRI volumes. On a cohort of 108 studies, the levelset MFLAAM yielded a mean Dice accuracy of 88% ± 5%, and a mean surface error of 1.5 mm ± .8 mm with a segmentation time of 150/s per volume. In comparison, a state of the art AAM yielded mean Dice and surface error values of 86% ± 9% and 1.6 mm ± 1.0 mm, respectively. The differences with respect to our levelset-based MFLAAM model are statistically significant (p <; .05). In addition, our results were in most cases superior to several recent state of the art prostate MRI segmentation methods.

A magnetic resonance spectroscopy driven initialization scheme for active shape model based prostate segmentation

Segmentation of the prostate boundary on clinical images is useful in a large number of applications including calculation of prostate volume pre- and post-treatment, to detect extra-capsular spread, and for creating patient-specific anatomical models. Manual segmentation of the prostate boundary is, however, time consuming and subject to inter- and intra-reader variability. T2-weighted (T2-w) magnetic resonance (MR) structural imaging (MRI) and MR spectroscopy (MRS) have recently emerged as promising modalities for detection of prostate cancer in vivo. MRS data consists of spectral signals measuring relative metabolic concentrations, and the metavoxels near the prostate have distinct spectral signals from metavoxels outside the prostate. Active Shape Models (ASMs) have become very popular segmentation methods for biomedical imagery. However, ASMs require careful initialization and are extremely sensitive to model initialization. The primary contribution of this paper is a scheme to automatically initialize an ASM for prostate segmentation on endorectal in vivo multi-protocol MRI via automated identification of MR spectra that lie within the prostate. A replicated clustering scheme is employed to distinguish prostatic from extra-prostatic MR spectra in the midgland. The spatial locations of the prostate spectra so identified are used as the initial ROI for a 2D ASM. The midgland initializations are used to define a ROI that is then scaled in 3D to cover the base and apex of the prostate. A multi-feature ASM employing statistical texture features is then used to drive the edge detection instead of just image intensity information alone. Quantitative comparison with another recent ASM initialization method by Cosio showed that our scheme resulted in a superior average segmentation performance on a total of 388 2D MRI sections obtained from 32 3D endorectal in vivo patient studies. Initialization of a 2D ASM via our MRS-based clustering scheme resulted in an average overlap accuracy (true positive ratio) of 0.60, while the scheme of Cosio yielded a corresponding average accuracy of 0.56 over 388 2D MR image sections. During an ASM segmentation, using no initialization resulted in an overlap of 0.53, using the Cosio based methodology resulted in an overlap of 0.60, and using the MRS-based methodology resulted in an overlap of 0.67, with a paired Students t-test indicating statistical significance to a high degree for all results. We also show that the final ASM segmentation result is highly correlated (as high as 0.90) to the initialization scheme.

Accurate prostate volume estimation using multifeature active shape models on T2-weighted MRI.

RATIONALE AND OBJECTIVES Accurate prostate volume estimation is useful for calculating prostate-specific antigen density and in evaluating posttreatment response. In the clinic, prostate volume estimation involves modeling the prostate as an ellipsoid or a spheroid from transrectal ultrasound, or T2-weighted magnetic resonance imaging (MRI). However, this requires some degree of manual intervention, and may not always yield accurate estimates. In this article, we present a multifeature active shape model (MFA) based segmentation scheme for estimating prostate volume from in vivo T2-weighted MRI. MATERIALS AND METHODS We aim to automatically determine the location of the prostate boundary on in vivo T2-weighted MRI, and subsequently determine the area of the prostate on each slice. The resulting planimetric areas are aggregated to yield the volume of the prostate for a given patient. Using a set of training images, the MFA learns the most discriminating statistical texture descriptors of the prostate boundary via a forward feature selection algorithm. After identification of the optimal image features, the MFA is deformed to accurately fit the prostate border. An expert radiologist segmented the prostate boundary on each slice and the planimetric aggregation of the enclosed areas yielded the ground truth prostate volume estimate. The volume estimation obtained via the MFA was then compared against volume estimations obtained via the ellipsoidal, Myschetzky, and prolated spheroids models. RESULTS We evaluated our MFA volume estimation method on a total 45 T2-weighted in vivo MRI studies, corresponding to both 1.5 Tesla and 3.0 Tesla field strengths. The results revealed that the ellipsoidal, Myschetzky, and prolate spheroid models overestimated prostate volumes, with volume fractions of 1.14, 1.53, and 1.96, respectively. By comparison, the MFA yielded a mean volume fraction of 1.05, evaluated using a fivefold cross-validation scheme. A correlation with the ground truth volume estimations showed that the MFA had an r(2) value of 0.82, whereas the clinical volume estimation schemes had a maximum value of 0.70. CONCLUSIONS Our MFA scheme involves minimal user intervention, is computationally efficient and results in volume estimations more accurate than state of the art clinical models.

Integrating Structural and Functional Imaging for Computer Assisted Detection of Prostate Cancer on Multi-Protocol In Vivo 3 Tesla MRI

Screening and detection of prostate cancer (CaP) currently lacks an image-based protocol which is reflected in the high false negative rates currently associated with blinded sextant biopsies. Multi-protocol magnetic resonance imaging (MRI) offers high resolution functional and structural data about internal body structures (such as the prostate). In this paper we present a novel comprehensive computer-aided scheme for CaP detection from high resolution in vivo multi-protocol MRI by integrating functional and structural information obtained via dynamic-contrast enhanced (DCE) and T2-weighted (T2-w) MRI, respectively. Our scheme is fully-automated and comprises (a) prostate segmentation, (b) multimodal image registration, and (c) data representation and multi-classifier modules for information fusion. Following prostate boundary segmentation via an improved active shape model, the DCE/T2-w protocols and the T2-w/ex vivo histological prostatectomy specimens are brought into alignment via a deformable, multi-attribute registration scheme. T2-w/histology alignment allows for the mapping of true CaP extent onto the in vivo MRI, which is used for training and evaluation of a multi-protocol MRI CaP classifier. The meta-classifier used is a random forest constructed by bagging multiple decision tree classifiers, each trained individually on T2-w structural, textural and DCE functional attributes. 3-fold classifier cross validation was performed using a set of 18 images derived from 6 patient datasets on a per-pixel basis. Our results show that the results of CaP detection obtained from integration of T2-w structural textural data and DCE functional data (area under the ROC curve of 0.815) significantly outperforms detection based on either of the individual modalities (0.704 (T2-w) and 0.682 (DCE)). It was also found that a meta-classifier trained directly on integrated T2-w and DCE data (data-level integration) significantly outperformed a decision-level meta-classifier, constructed by combining the classifier outputs from the individual T2-w and DCE channels.

A Comprehensive Segmentation, Registration, and Cancer Detection Scheme on 3 Tesla In Vivo Prostate DCE-MRI

Recently, high resolution 3 Tesla (T) Dynamic Contrast-Enhanced MRI (DCE-MRI) of the prostate has emerged as a promising modality for detecting prostate cancer (CaP). Computer-aided diagnosis (CAD) schemes for DCE-MRI data have thus far been primarily developed for breast cancer and typically involve model fitting of dynamic intensity changes as a function of contrast agent uptake by the lesion. Comparatively there is relatively little work in developing CAD schemes for prostate DCE-MRI. In this paper, we present a novel unsupervised detection scheme for CaP from 3 T DCE-MRI which comprises 3 distinct steps. First, a multi-attribute active shape model is used to automatically segment the prostate boundary from 3 T in vivo MR imagery. A robust multimodal registration scheme is then used to non-linearly align corresponding whole mount histological and DCE-MRI sections from prostatectomy specimens to determine the spatial extent of CaP. Non-linear dimensionality reduction schemes such as locally linear embedding (LLE) have been previously shown to be useful in projecting such high dimensional biomedical data into a lower dimensional subspace while preserving the non-linear geometry of the data manifold. DCE-MRI data is embedded via LLE and then classified via unsupervised consensus clustering to identify distinct classes. Quantitative evaluation on 21 histology-MRI slice pairs against registered CaP ground truth estimates yielded a maximum CaP detection accuracy of 77.20% while the popular three time point (3TP) scheme yielded an accuracy of 67.37%.

Concurrent segmentation of the prostate on MRI and CT via linked statistical shape models for radiotherapy planning.

PURPOSE Prostate gland segmentation is a critical step in prostate radiotherapy planning, where dose plans are typically formulated on CT. Pretreatment MRI is now beginning to be acquired at several medical centers. Delineation of the prostate on MRI is acknowledged as being significantly simpler to perform, compared to delineation on CT. In this work, the authors present a novel framework for building a linked statistical shape model (LSSM), a statistical shape model (SSM) that links the shape variation of a structure of interest (SOI) across multiple imaging modalities. This framework is particularly relevant in scenarios where accurate boundary delineations of the SOI on one of the modalities may not be readily available, or difficult to obtain, for training a SSM. In this work the authors apply the LSSM in the context of multimodal prostate segmentation for radiotherapy planning, where the prostate is concurrently segmented on MRI and CT. METHODS The framework comprises a number of logically connected steps. The first step utilizes multimodal registration of MRI and CT to map 2D boundary delineations of the prostate from MRI onto corresponding CT images, for a set of training studies. Hence, the scheme obviates the need for expert delineations of the gland on CT for explicitly constructing a SSM for prostate segmentation on CT. The delineations of the prostate gland on MRI and CT allows for 3D reconstruction of the prostate shape which facilitates the building of the LSSM. In order to perform concurrent prostate MRI and CT segmentation using the LSSM, the authors employ a region-based level set approach where the authors deform the evolving prostate boundary to simultaneously fit to MRI and CT images in which voxels are classified to be either part of the prostate or outside the prostate. The classification is facilitated by using a combination of MRI-CT probabilistic spatial atlases and a random forest classifier, driven by gradient and Haar features. RESULTS The authors acquire a total of 20 MRI-CT patient studies and use the leave-one-out strategy to train and evaluate four different LSSMs. First, a fusion-based LSSM (fLSSM) is built using expert ground truth delineations of the prostate on MRI alone, where the ground truth for the gland on CT is obtained via coregistration of the corresponding MRI and CT slices. The authors compare the fLSSM against another LSSM (xLSSM), where expert delineations of the gland on both MRI and CT are employed in the model building; xLSSM representing the idealized LSSM. The authors also compare the fLSSM against an exclusive CT-based SSM (ctSSM), built from expert delineations of the gland on CT alone. In addition, two LSSMs trained using trainee delineations (tLSSM) on CT are compared with the fLSSM. The results indicate that the xLSSM, tLSSMs, and the fLSSM perform equivalently, all of them out-performing the ctSSM. CONCLUSIONS The fLSSM provides an accurate alternative to SSMs that require careful expert delineations of the SOI that may be difficult or laborious to obtain. Additionally, the fLSSM has the added benefit of providing concurrent segmentations of the SOI on multiple imaging modalities.

A multi-modal prostate segmentation scheme by combining spectral clustering and active shape models

Segmentation of the prostate boundary on clinical images is useful in a large number of applications including calculating prostate volume during biopsy, tumor estimation, and treatment planning. Manual segmentation of the prostate boundary is, however, time consuming and subject to inter- and intra-reader variability. Magnetic Resonance (MR) imaging (MRI) and MR Spectroscopy (MRS) have recently emerged as promising modalities for detection of prostate cancer in vivo. In this paper we present a novel scheme for accurate and automated prostate segmentation on in vivo 1.5 Tesla multi-modal MRI studies. The segmentation algorithm comprises two steps: (1) A hierarchical unsupervised spectral clustering scheme using MRS data to isolate the region of interest (ROI) corresponding to the prostate, and (2) an Active Shape Model (ASM) segmentation scheme where the ASM is initialized within the ROI obtained in the previous step. The hierarchical MRS clustering scheme in step 1 identifies spectra corresponding to locations within the prostate in an iterative fashion by discriminating between potential prostate and non-prostate spectra in a lower dimensional embedding space. The spatial locations of the prostate spectra so identified are used as the initial ROI for the ASM. The ASM is trained by identifying user-selected landmarks on the prostate boundary on T2 MRI images. Boundary points on the prostate are identified using mutual information (MI) as opposed to the traditional Mahalanobis distance, and the trained ASM is deformed to fit the boundary points so identified. Cross validation on 150 prostate MRI slices yields an average segmentation sensitivity, specificity, overlap, and positive predictive value of 89, 86, 83, and 93&percent; respectively. We demonstrate that the accurate initialization of the ASM via the spectral clustering scheme is necessary for automated boundary extraction. Our method is fully automated, robust to system parameters, and computationally efficient.

Simultaneous segmentation of prostatic zones using Active Appearance Models with multiple coupled levelsets

In this work we present an improvement to the popular Active Appearance Model (AAM) algorithm, that we call the Multiple-Levelset AAM (MLA). The MLA can simultaneously segment multiple objects, and makes use of multiple levelsets, rather than anatomical landmarks, to define the shapes. AAMs traditionally define the shape of each object using a set of anatomical landmarks. However, landmarks can be difficult to identify, and AAMs traditionally only allow for segmentation of a single object of interest. The MLA, which is a landmark independent AAM, allows for levelsets of multiple objects to be determined and allows for them to be coupled with image intensities. This gives the MLA the flexibility to simulataneously segmentation multiple objects of interest in a new image. In this work we apply the MLA to segment the prostate capsule, the prostate peripheral zone (PZ), and the prostate central gland (CG), from a set of 40 endorectal, T2-weighted MRI images. The MLA system we employ in this work leverages a hierarchical segmentation framework, so constructed as to exploit domain specific attributes, by utilizing a given prostate segmentation to help drive the segmentations of the CG and PZ, which are embedded within the prostate. Our coupled MLA scheme yielded mean Dice accuracy values of .81, .79 and .68 for the prostate, CG, and PZ, respectively using a leave-one-out cross validation scheme over 40 patient studies. When only considering the midgland of the prostate, the mean DSC values were .89, .84, and .76 for the prostate, CG, and PZ respectively.