Girona Magnetic Resonance Center

Girona, Spain

Girona Magnetic Resonance Center

Girona, Spain
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Ghose S.,CSIRO | Oliver A.,University of Girona | Mitra J.,CSIRO | Marti R.,University of Girona | And 6 more authors.
Medical Image Analysis | Year: 2013

Prostate segmentation aids in prostate volume estimation, multi-modal image registration, and to create patient specific anatomical models for surgical planning and image guided biopsies. However, manual segmentation is time consuming and suffers from inter-and intra-observer variabilities. Low contrast images of trans rectal ultrasound and presence of imaging artifacts like speckle, micro-calcifications, and shadow regions hinder computer aided automatic or semi-automatic prostate segmentation. In this paper, we propose a prostate segmentation approach based on building multiple mean parametric models derived from principal component analysis of shape and posterior probabilities in a multi-resolution framework. The model parameters are then modified with the prior knowledge of the optimization space to achieve optimal prostate segmentation. In contrast to traditional statistical models of shape and intensity priors, we use posterior probabilities of the prostate region determined from random forest classification to build our appearance model, initialize and propagate our model. Furthermore, multiple mean models derived from spectral clustering of combined shape and appearance parameters are applied in parallel to improve segmentation accuracies. The proposed method achieves mean Dice similarity coefficient value of 0.91. ±. 0.09 for 126 images containing 40 images from the apex, 40 images from the base and 46 images from central regions in a leave-one-patient-out validation framework. The mean segmentation time of the procedure is 0.67. ±. 0.02. s. © 2013 Elsevier B.V.

Mitra J.,University of Burgundy | Mitra J.,University of Girona | Kato Z.,University of Szeged | Marti R.,University of Girona | And 8 more authors.
Medical Image Analysis | Year: 2012

This paper presents a novel method for non-rigid registration of transrectal ultrasound and magnetic resonance prostate images based on a non-linear regularized framework of point correspondences obtained from a statistical measure of shape-contexts. The segmented prostate shapes are represented by shape-contexts and the Bhattacharyya distance between the shape representations is used to find the point correspondences between the 2D fixed and moving images. The registration method involves parametric estimation of the non-linear diffeomorphism between the multimodal images and has its basis in solving a set of non-linear equations of thin-plate splines. The solution is obtained as the least-squares solution of an over-determined system of non-linear equations constructed by integrating a set of non-linear functions over the fixed and moving images. However, this may not result in clinically acceptable transformations of the anatomical targets. Therefore, the regularized bending energy of the thin-plate splines along with the localization error of established correspondences should be included in the system of equations. The registration accuracies of the proposed method are evaluated in 20 pairs of prostate mid-gland ultrasound and magnetic resonance images. The results obtained in terms of Dice similarity coefficient show an average of 0.980 ± 0.004, average 95% Hausdorff distance of 1.63 ± 0.48. mm and mean target registration and target localization errors of 1.60 ± 1.17. mm and 0.15 ± 0.12. mm respectively. © 2012 Elsevier B.V.

Ghose S.,University of Girona | Ghose S.,University of Burgundy | Oliver A.,University of Girona | Marti R.,University of Girona | And 7 more authors.
Computer Methods and Programs in Biomedicine | Year: 2012

Prostate segmentation is a challenging task, and the challenges significantly differ from one imaging modality to another. Low contrast, speckle, micro-calcifications and imaging artifacts like shadow poses serious challenges to accurate prostate segmentation in transrectal ultrasound (TRUS) images. However in magnetic resonance (MR) images, superior soft tissue contrast highlights large variability in shape, size and texture information inside the prostate. In contrast poor soft tissue contrast between prostate and surrounding tissues in computed tomography (CT) images pose a challenge in accurate prostate segmentation. This article reviews the methods developed for prostate gland segmentation TRUS, MR and CT images, the three primary imaging modalities that aids prostate cancer diagnosis and treatment. The objective of this work is to study the key similarities and differences among the different methods, highlighting their strengths and weaknesses in order to assist in the choice of an appropriate segmentation methodology. We define a new taxonomy for prostate segmentation strategies that allows first to group the algorithms and then to point out the main advantages and drawbacks of each strategy. We provide a comprehensive description of the existing methods in all TRUS, MR and CT modalities, highlighting their key-points and features. Finally, a discussion on choosing the most appropriate segmentation strategy for a given imaging modality is provided. A quantitative comparison of the results as reported in literature is also presented. © 2012 Elsevier Ireland Ltd.

Llado X.,University of Girona | Oliver A.,University of Girona | Cabezas M.,University of Girona | Freixenet J.,University of Girona | And 5 more authors.
Information Sciences | Year: 2012

Automatic segmentation of multiple sclerosis (MS) lesions in brain MRI has been widely investigated in recent years with the goal of helping MS diagnosis and patient follow-up. However, the performance of most of the algorithms still falls far below expert expectations. In this paper, we review the main approaches to automated MS lesion segmentation. The main features of the segmentation algorithms are analysed and the most recent important techniques are classified into different strategies according to their main principle, pointing out their strengths and weaknesses and suggesting new research directions. A qualitative and quantitative comparison of the results of the approaches analysed is also presented. Finally, possible future approaches to MS lesion segmentation are discussed. © 2011 Elsevier Inc. All rights reserved.

Diez Y.,University of Girona | Oliver A.,University of Girona | Cabezas M.,University of Girona | Valverde S.,University of Girona | And 5 more authors.
Neuroinformatics | Year: 2014

Registration is a key step in many automatic brain Magnetic Resonance Imaging (MRI) applications. In this work we focus on longitudinal registration of brain MRI for Multiple Sclerosis (MS) patients. First of all, we analyze the effect that MS lesions have on registration by synthetically eliminating some of the lesions. Our results show how a widely used method for longitudinal registration such as rigid registration is practically unconcerned by the presence of MS lesions while several non-rigid registration methods produce outputs that are significantly different. We then focus on assessing which is the best registration method for longitudinal MRI images of MS patients. In order to analyze the results obtained for all studied criteria, we use both descriptive statistics and statistical inference: one way ANOVA, pairwise t-tests and permutation tests. © 2013 Springer Science+Business Media New York.

Valverde S.,University of Girona | Oliver A.,University of Girona | Diez Y.,University of Girona | Cabezas M.,University of Barcelona | And 4 more authors.
American Journal of Neuroradiology | Year: 2015

BACKGROUND AND PURPOSE: The accuracy of automatic tissue segmentation methods can be affected by the presence of hypointense white matter lesions during the tissue segmentation process. Our aim was to evaluate the impact of MS white matter lesions on the brain tissue measurements of 6 well-known segmentation techniques. These include straightforward techniques such as Artificial Neural Network and fuzzy C-means as well as more advanced techniques such as the Fuzzy And Noise Tolerant Adaptive Segmentation Method, fMRI of the Brain Automated Segmentation Tool, SPM5, and SPM8. MATERIALS AND METHODS: Thirty T1-weighted images from patients with MS from 3 different scanners were segmented twice, first including white matter lesions and then masking the lesions before segmentation and relabeling as WM afterward. The differences in total tissue volume and tissue volume outside the lesion regions were computed between the images by using the 2 methodologies. RESULTS: Total gray matter volume was overestimated by all methods when lesion volume increased. The tissue volume outside the lesion regions was also affected by white matter lesions with differences up to 20 cm3 on images with a high lesion load (≈50 cm3). SPM8 and Fuzzy And Noise Tolerant Adaptive Segmentation Method were the methods less influenced by white matter lesions, whereas the effect of white matter lesions was more prominent on fuzzy C-means and the fMRI of the Brain Automated Segmentation Tool. CONCLUSIONS: Although lesions were removed after segmentation to avoid their impact on tissue segmentation, the methods still overestimated GM tissue in most cases. This finding is especially relevant because on images with high lesion load, this bias will most likely distort actual tissue atrophy measurements.

Roura E.,University of Girona | Oliver A.,University of Girona | Cabezas M.,University of Girona | Vilanova J.C.,Girona Magnetic Resonance Center | And 3 more authors.
Computer Methods and Programs in Biomedicine | Year: 2014

Brain extraction, also known as skull stripping, is one of the most important preprocessing steps for many automatic brain image analysis. In this paper we present a new approach called Multispectral Adaptive Region Growing Algorithm (MARGA) to perform the skull stripping process. MARGA is based on a region growing (RG) algorithm which uses the complementary information provided by conventional magnetic resonance images (MRI) such as T1-weighted and T2-weighted to perform the brain segmentation. MARGA can be seen as an extension of the skull stripping method proposed by Park and Lee (2009) [1], enabling their use in both axial views and low quality images. Following the same idea, we first obtain seed regions that are then spread using a 2D RG algorithm which behaves differently in specific zones of the brain. This adaptation allows to deal with the fact that middle MRI slices have better image contrast between the brain and non-brain regions than superior and inferior brain slices where the contrast is smaller. MARGA is validated using three different databases: 10 simulated brains from the BrainWeb database; 2 data sets from the National Alliance for Medical Image Computing (NAMIC) database, the first one consisting in 10 normal brains and 10 brains of schizophrenic patients acquired with a 3. T GE scanner, and the second one consisting in 5 brains from lupus patients acquired with a 3. T Siemens scanner; and 10 brains of multiple sclerosis patients acquired with a 1.5. T scanner. We have qualitatively and quantitatively compared MARGA with the well-known Brain Extraction Tool (BET), Brain Surface Extractor (BSE) and Statistical Parametric Mapping (SPM) approaches. The obtained results demonstrate the validity of MARGA, outperforming the results of those standard techniques. © 2013 Elsevier Ireland Ltd.

Ganiler O.,University of Girona | Oliver A.,University of Girona | Diez Y.,University of Girona | Freixenet J.,University of Girona | And 5 more authors.
Neuroradiology | Year: 2014

Introduction: Time-series analysis of magnetic resonance images (MRI) is of great value for multiple sclerosis (MS) diagnosis and follow-up. In this paper, we present an unsupervised subtraction approach which incorporates multisequence information to deal with the detection of new MS lesions in longitudinal studies. Methods: The proposed pipeline for detecting new lesions consists of the following steps: skull stripping, bias field correction, histogram matching, registration, white matter masking, image subtraction, automated thresholding, and postprocessing. We also combine the results of PD-w and T2-w images to reduce false positive detections. Results: Experimental tests are performed in 20 MS patients with two temporal studies separated 12 (12M) or 48 (48M) months in time. The pipeline achieves very good performance obtaining an overall sensitivity of 0.83 and 0.77 with a false discovery rate (FDR) of 0.14 and 0.18 for the 12M and 48M datasets, respectively. The most difficult situation for the pipeline is the detection of very small lesions where the obtained sensitivity is lower and the FDR higher. Conclusion: Our fully automated approach is robust and accurate, allowing detection of new appearing MS lesions. We believe that the pipeline can be applied to large collections of images and also be easily adapted to monitor other brain pathologies. © 2014 Springer-Verlag.

Llado X.,University of Girona | Ganiler O.,University of Girona | Oliver A.,University of Girona | Marti R.,University of Girona | And 5 more authors.
Neuroradiology | Year: 2012

Introduction Multiple sclerosis (MS) is a serious disease typically occurring in the brain whose diagnosis and efficacy of treatment monitoring are vital. Magnetic resonance imaging (MRI) is frequently used in serial brain imaging due to the rich and detailed information provided. Methods Time-series analysis of images is widely used for MS diagnosis and patient follow-up. However, conventional manual methods are time-consuming, subjective, and errorprone. Thus, the development of automated techniques for the detection and quantification of MS lesions is a major challenge. Results This paper presents an up-to-date review of the approaches which deal with the time-series analysis of brain MRI for detecting active MS lesions and quantifying lesion load change. We provide a comprehensive reference source for researchers in which several approaches to change detection and quantification of MS lesions are investigated and classified. We also analyze the results provided by the approaches, discuss open problems, and point out possible future trends. Conclusion Lesion detection approaches are required for the detection of static lesions and for diagnostic purposes, while either quantification of detected lesions or change detection algorithms are needed to follow up MS patients. However, there is not yet a single approach that can emerge as a standard for the clinical practice, automatically providing an accurate MS lesion evolution quantification. Future trends will focus on combining the lesion detection in single studies with the analysis of the change detection in serial MRI. © 2011 Springer-Verlag.

Roura E.,University of Girona | Oliver A.,University of Girona | Cabezas M.,University of Barcelona | Valverde S.,University of Girona | And 5 more authors.
Neuroradiology | Year: 2015

Introduction: Lesion segmentation plays an important role in the diagnosis and follow-up of multiple sclerosis (MS). This task is very time-consuming and subject to intra- and inter-rater variability. In this paper, we present a new tool for automated MS lesion segmentation using T1w and fluid-attenuated inversion recovery (FLAIR) images. Methods: Our approach is based on two main steps, initial brain tissue segmentation according to the gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) performed in T1w images, followed by a second step where the lesions are segmented as outliers to the normal apparent GM brain tissue on the FLAIR image. Results: The tool has been validated using data from more than 100 MS patients acquired with different scanners and at different magnetic field strengths. Quantitative evaluation provided a better performance in terms of precision while maintaining similar results on sensitivity and Dice similarity measures compared with those of other approaches. Conclusion: Our tool is implemented as a publicly available SPM8/12 extension that can be used by both the medical and research communities. © 2015, Springer-Verlag Berlin Heidelberg.

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