Optimizing the Dice Score and Jaccard Index for Medical Image Segmentation: Theory & Practice

The Dice score and Jaccard index are commonly used metrics for the evaluation of segmentation tasks in medical imaging. Convolutional neural networks trained for image segmentation tasks are usually optimized for (weighted) cross-entropy. This introduces an adverse discrepancy between the learning optimization objective (the loss) and the end target metric. Recent works in computer vision have proposed soft surrogates to alleviate this discrepancy and directly optimize the desired metric, either through relaxations (soft-Dice, soft-Jaccard) or submodular optimization (Lov\'asz-softmax). The aim of this study is two-fold. First, we investigate the theoretical differences in a risk minimization framework and question the existence of a weighted cross-entropy loss with weights theoretically optimized to surrogate Dice or Jaccard. Second, we empirically investigate the behavior of the aforementioned loss functions w.r.t. evaluation with Dice score and Jaccard index on five medical segmentation tasks. Through the application of relative approximation bounds, we show that all surrogates are equivalent up to a multiplicative factor, and that no optimal weighting of cross-entropy exists to approximate Dice or Jaccard measures. We validate these findings empirically and show that, while it is important to opt for one of the target metric surrogates rather than a cross-entropy-based loss, the choice of the surrogate does not make a statistical difference on a wide range of medical segmentation tasks.Comment: MICCAI 201

Spatial based Expectation Maximizing (EM)

<p>Abstract</p> <p>Background</p> <p>Expectation maximizing (EM) is one of the common approaches for image segmentation.</p> <p>Methods</p> <p>an improvement of the EM algorithm is proposed and its effectiveness for MRI brain image segmentation is investigated. In order to improve EM performance, the proposed algorithms incorporates neighbourhood information into the clustering process. At first, average image is obtained as neighbourhood information and then it is incorporated in clustering process. Also, as an option, user-interaction is used to improve segmentation results. Simulated and real MR volumes are used to compare the efficiency of the proposed improvement with the existing neighbourhood based extension for EM and FCM.</p> <p>Results</p> <p>the findings show that the proposed algorithm produces higher similarity index.</p> <p>Conclusions</p> <p>experiments demonstrate the effectiveness of the proposed algorithm in compare to other existing algorithms on various noise levels.</p

Articulated Whole-Body Atlases for Small Animal Image Analysis: Construction and Applications

Bone and mineral researc

Neurexin-1 and Frontal Lobe White Matter: An Overlapping Intermediate Phenotype for Schizophrenia and Autism Spectrum Disorders

Background: Structural variation in the neurexin-1 (NRXN1) gene increases risk for both autism spectrum disorders (ASD) and schizophrenia. However, the manner in which NRXN1 gene variation may be related to brain morphology to confer risk for ASD or schizophrenia is unknown. Method/Principal Findings: 53 healthy individuals between 18–59 years of age were genotyped at 11 single nucleotide polymorphisms of the NRXN1 gene. All subjects received structural MRI scans, which were processed to determine cortical gray and white matter lobar volumes, and volumes of striatal and thalamic structures. Each subject’s sensorimotor function was also assessed. The general linear model was used to calculate the influence of genetic variation on neural and cognitive phenotypes. Finally, in silico analysis was conducted to assess potential functional relevance of any polymorphisms associated with brain measures. A polymorphism located in the 39 untranslated region of NRXN1 significantly influenced white matter volumes in whole brain and frontal lobes after correcting for total brain volume, age and multiple comparisons. Follow-up in silico analysis revealed that this SNP is a putative microRNA binding site that may be of functional significance in regulating NRXN1 expression. This variant also influenced sensorimotor performance, a neurocognitive function impaired in both ASD and schizophrenia. Conclusions: Our findings demonstrate that the NRXN1 gene, a vulnerability gene for SCZ and ASD, influences brai

3 Tesla multiparametric MRI for GTV-definition of Dominant Intraprostatic Lesions in patients with Prostate Cancer – an interobserver variability study

PURPOSE: To evaluate the interobserver variability of gross tumor volume (GTV) - delineation of Dominant Intraprostatic Lesions (DIPL) in patients with prostate cancer using published MRI criteria for multiparametric MRI at 3 Tesla by 6 different observers. MATERIAL AND METHODS: 90 GTV-datasets based on 15 multiparametric MRI sequences (T2w, diffusion weighted (DWI) and dynamic contrast enhanced (DCE)) of 5 patients with prostate cancer were generated for GTV-delineation of DIPL by 6 observers. The reference GTV-dataset was contoured by a radiologist with expertise in diagnostic imaging of prostate cancer using MRI. Subsequent GTV-delineation was performed by 5 radiation oncologists who received teaching of MRI-features of primary prostate cancer before starting contouring session. GTV-datasets were contoured using Oncentra Masterplan® and iplan® Net. For purposes of comparison GTV-datasets were imported to the Artiview® platform (Aquilab®), GTV-values and the similarity indices or Kappa indices (KI) were calculated with the postulation that a KI > 0.7 indicates excellent, a KI > 0.6 to < 0.7 substantial and KI > 0.5 to < 0.6 moderate agreement. Additionally all observers rated difficulties of contouring for each MRI-sequence using a 3 point rating scale (1 = easy to delineate, 2 = minor difficulties, 3 = major difficulties). RESULTS: GTV contouring using T2w (KI-T2w = 0.61) and DCE images (KI-DCE = 0.63) resulted in substantial agreement. GTV contouring using DWI images resulted in moderate agreement (KI-DWI = 0.51). KI-T2w and KI-DCE was significantly higher than KI-DWI (p = 0.01 and p = 0.003). Degree of difficulty in contouring GTV was significantly lower using T2w and DCE compared to DWI-sequences (both p < 0.0001). Analysis of delineation differences revealed inadequate comparison of functional (DWI, DCE) to anatomical sequences (T2w) and lack of awareness of non-specific imaging findings as a source of erroneous delineation. CONCLUSIONS: Using T2w and DCE sequences at 3 Tesla for GTV-definition of DIPL in prostate cancer patients by radiation oncologists with knowledge of MRI features results in substantial agreement compared to an experienced MRI-radiologist, but for radiotherapy purposes higher KI are desirable, strengthen the need for expert surveillance. DWI sequence for GTV delineation was considered as difficult in application

Hierarchical multivariate covariance analysis of metabolic connectivity

Conventional brain connectivity analysis is typically based on the assessment of interregional correlations. Given that correlation coefficients are derived from both covariance and variance, group differences in covariance may be obscured by differences in the variance terms. To facilitate a comprehensive assessment of connectivity, we propose a unified statistical framework that interrogates the individual terms of the correlation coefficient. We have evaluated the utility of this method for metabolic connectivity analysis using [18F]2-fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. As an illustrative example of the utility of this approach, we examined metabolic connectivity in angular gyrus and precuneus seed regions of mild cognitive impairment (MCI) subjects with low and high β-amyloid burdens. This new multivariate method allowed us to identify alterations in the metabolic connectome, which would not have been detected using classic seed-based correlation analysis. Ultimately, this novel approach should be extensible to brain network analysis and broadly applicable to other imaging modalities, such as functional magnetic resonance imaging (MRI).© 2014,SAGE Publication