Towards personalized diagnosis of Glioblastoma in Fluid-attenuated inversion recovery (FLAIR) by topological interpretable machine learning

Glioblastoma multiforme (GBM) is a fast-growing and highly invasive brain tumour, it tends to occur in adults between the ages of 45 and 70 and it accounts for 52 percent of all primary brain tumours. Usually, GBMs are detected by magnetic resonance images (MRI). Among MRI, Fluid-attenuated inversion recovery (FLAIR) sequence produces high quality digital tumour representation. Fast detection and segmentation techniques are needed for overcoming subjective medical doctors (MDs) judgment. In the present investigation, we intend to demonstrate by means of numerical experiments that topological features combined with textural features can be enrolled for GBM analysis and morphological characterization on FLAIR. To this extent, we have performed three numerical experiments. In the first experiment, Topological Data Analysis (TDA) of a simplified 2D tumour growth mathematical model had allowed to understand the bio-chemical conditions that facilitate tumour growth: the higher the concentration of chemical nutrients the more virulent the process. In the second experiment topological data analysis was used for evaluating GBM temporal progression on FLAIR recorded within 90 days following treatment (e.g., chemo-radiation therapy - CRT) completion and at progression. The experiment had confirmed that persistent entropy is a viable statistics for monitoring GBM evolution during the follow-up period. In the third experiment we had developed a novel methodology based on topological and textural features and automatic interpretable machine learning for automatic GBM classification on FLAIR. The algorithm reached a classification accuracy up to the 97%.Comment: 22 pages; 16 figure

MRI Radiomic Signature of White Matter Hyperintensities Is Associated With Clinical Phenotypes

Objective: Neuroimaging measurements of brain structural integrity are thought to be surrogates for brain health, but precise assessments require dedicated advanced image acquisitions. By means of quantitatively describing conventional images, radiomic analyses hold potential for evaluating brain health. We sought to: (1) evaluate radiomics to assess brain structural integrity by predicting white matter hyperintensities burdens (WMH) and (2) uncover associations between predictive radiomic features and clinical phenotypes. Methods: We analyzed a multi-site cohort of 4,163 acute ischemic strokes (AIS) patients with T2-FLAIR MR images with total brain and WMH segmentations. Radiomic features were extracted from normal-appearing brain tissue (brain mask-WMH mask). Radiomics-based prediction of personalized WMH burden was done using ElasticNet linear regression. We built a radiomic signature of WMH with stable selected features predictive of WMH burden and then related this signature to clinical variables using canonical correlation analysis (CCA). Results: Radiomic features were predictive of WMH burden (R-2 = 0.855 +/- 0.011). Seven pairs of canonical variates (CV) significantly correlated the radiomics signature of WMH and clinical traits with respective canonical correlations of 0.81, 0.65, 0.42, 0.24, 0.20, 0.15, and 0.15 (FDR-corrected p-values(CV1-6) < 0.001, p-value(CV7) = 0.012). The clinical CV1 was mainly influenced by age, CV2 by sex, CV3 by history of smoking and diabetes, CV4 by hypertension, CV5 by atrial fibrillation (AF) and diabetes, CV6 by coronary artery disease (CAD), and CV7 by CAD and diabetes. Conclusion: Radiomics extracted from T2-FLAIR images of AIS patients capture microstructural damage of the cerebral parenchyma and correlate with clinical phenotypes, suggesting different radiographical textural abnormalities per cardiovascular risk profile. Further research could evaluate radiomics to predict the progression of WMH and for the follow-up of stroke patients' brain health.Peer reviewe

MRI radiomic signature of white matter hyperintensities is associated with clinical phenotypes

Objective: Neuroimaging measurements of brain structural integrity are thought to be surrogates for brain health, but precise assessments require dedicated advanced image acquisitions. By means of quantitatively describing conventional images, radiomic analyses hold potential for evaluating brain health. We sought to: (1) evaluate radiomics to assess brain structural integrity by predicting white matter hyperintensities burdens (WMH) and (2) uncover associations between predictive radiomic features and clinical phenotypes. Methods: We analyzed a multi-site cohort of 4,163 acute ischemic strokes (AIS) patients with T2-FLAIR MR images with total brain and WMH segmentations. Radiomic features were extracted from normal-appearing brain tissue (brain mask-WMH mask). Radiomics-based prediction of personalized WMH burden was done using ElasticNet linear regression. We built a radiomic signature of WMH with stable selected features predictive of WMH burden and then related this signature to clinical variables using canonical correlation analysis (CCA). Results: Radiomic features were predictive of WMH burden ( Conclusion: Radiomics extracted from T2-FLAIR images of AIS patients capture microstructural damage of the cerebral parenchyma and correlate with clinical phenotypes, suggesting different radiographical textural abnormalities per cardiovascular risk profile. Further research could evaluate radiomics to predict the progression of WMH and for the follow-up of stroke patients\u27 brain health

MRI Radiomic Signature of White Matter Hyperintensities Is Associated With Clinical Phenotypes

Objective: Neuroimaging measurements of brain structural integrity are thought to be surrogates for brain health, but precise assessments require dedicated advanced image acquisitions. By means of quantitatively describing conventional images, radiomic analyses hold potential for evaluating brain health. We sought to: (1) evaluate radiomics to assess brain structural integrity by predicting white matter hyperintensities burdens (WMH) and (2) uncover associations between predictive radiomic features and clinical phenotypes. Methods: We analyzed a multi-site cohort of 4,163 acute ischemic strokes (AIS) patients with T2-FLAIR MR images with total brain and WMH segmentations. Radiomic features were extracted from normal-appearing brain tissue (brain mask–WMH mask). Radiomics-based prediction of personalized WMH burden was done using ElasticNet linear regression. We built a radiomic signature of WMH with stable selected features predictive of WMH burden and then related this signature to clinical variables using canonical correlation analysis (CCA). Results: Radiomic features were predictive of WMH burden (R2 = 0.855 ± 0.011). Seven pairs of canonical variates (CV) significantly correlated the radiomics signature of WMH and clinical traits with respective canonical correlations of 0.81, 0.65, 0.42, 0.24, 0.20, 0.15, and 0.15 (FDR-corrected p-valuesCV1–6 < 0.001, p-valueCV7 = 0.012). The clinical CV1 was mainly influenced by age, CV2 by sex, CV3 by history of smoking and diabetes, CV4 by hypertension, CV5 by atrial fibrillation (AF) and diabetes, CV6 by coronary artery disease (CAD), and CV7 by CAD and diabetes. Conclusion: Radiomics extracted from T2-FLAIR images of AIS patients capture microstructural damage of the cerebral parenchyma and correlate with clinical phenotypes, suggesting different radiographical textural abnormalities per cardiovascular risk profile. Further research could evaluate radiomics to predict the progression of WMH and for the follow-up of stroke patients’ brain health

Structural MRI texture analysis for detecting Alzheimer's disease

Purpose:: Alzheimer’s disease (AD) has the highest worldwide prevalence of all neurodegenerative disorders, no cure, and low ratios of diagnosis accuracy at its early stage where treatments have some effect and can give some years of life quality to patients. This work aims to develop an automatic method to detect AD in 3 different stages, namely, control (CN), mild-cognitive impairment (MCI), and AD itself, using structural magnetic resonance imaging (sMRI). Methods:: A set of co-occurrence matrix and texture statistical measures (contrast, correlation, energy, homogeneity, entropy, variance, and standard deviation) were extracted from a two-level discrete wavelet transform decomposition of sMRI images. The discriminant capacity of the measures was analyzed and the most discriminant ones were selected to be used as features for feeding classical machine learning (cML) algorithms and a convolution neural network (CNN). Results:: The cML algorithms achieved the following classification accuracies: 93.3% for AD vs CN, 87.7% for AD vs MCI, 88.2% for CN vs MCI, and 75.3% for All vs All. The CNN achieved the following classification accuracies: 82.2% for AD vs CN, 75.4% for AD vs MCI, 83.8% for CN vs MCI, and 64% for All vs All. Conclusion:: In the evaluated cases, cML provided higher discrimination results than CNN. For the All vs All comparison, the proposedmethod surpasses by 4% the discrimination accuracy of the state-of-the-art methods that use structural MRI.info:eu-repo/semantics/publishedVersio

The multimodal Ganzfeld-induced altered state of consciousness induces decreased thalamo-cortical coupling

Different pharmacologic agents have been used to investigate the neuronal underpinnings of alterations in consciousness states, such as psychedelic substances. Special attention has been drawn to the role of thalamic filtering of cortical input. Here, we investigate the neuronal mechanisms underlying an altered state of consciousness (ASC) induced by a non-pharmacological procedure. During fMRI scanning, N=19 human participants were exposed to multimodal Ganzfeld stimulation, a technique of perceptual deprivation where participants are exposed to intense, unstructured, homogenous visual and auditory stimulation. Compared to pre- and post-resting-state scans, the Ganzfeld data displayed a progressive decoupling of the thalamus from the cortex. Furthermore, the Ganzfeld-induced ASC was characterized by increased eigenvector centrality in core regions of the default mode network (DMN). Together, these findings can be interpreted as an imbalance of sensory bottom-up signaling and internally-generated top-down signaling. This imbalance is antithetical to psychedelic-induced ASCs, where increased thalamo-cortical coupling and reduced DMN activity were observed

Advanced MRI methods for probing disease severity and functional decline in multiple sclerosis

Multiple sclerosis (MS) is a chronic and severe disease of the central nervous system characterized by complex pathology including inflammatory demyelination and neurodegeneration. MS impacts >2.8 million people worldwide, with most starting with a relapsing-remitting form (RRMS) in young adulthood, and many of them worsening to a secondary-progressive course (SPMS) despite treatment. So, there is a clear need for improved disease characterization. MRI is an ideal tool for non-invasive assessment of MS pathology, but there is still no established measure of disease activity and functional consequences. This project aims to overcome the challenge by developing novel imaging measures based on brain diffusion MRI and phase congruency texture analysis of conventional MRI. Through advanced modeling and analysis of clinically feasible brain MRI, this thesis investigates whether and how the derived measures differentiate MS pathology types and disease severity and predict functional outcomes in MS. The overall process has led to important technical innovations in several aspects. These include: innovative modeling of simple diffusion acquisitions to generate high angular resolution diffusion imaging (HARDI) measures; new optimization and harmonization techniques for diffusion MRI; innovative neural network models to create new diffusion data for comprehensive HARDI modeling; and novel methods and a graphic user interface for optimizing phase congruency analyses. Assisted by different machine learning methods, collective findings show that advanced measures from both diffusion MRI and phase congruency are highly sensitive to subtle differences in MS pathology, which differentiate disease severity between RRMS and SPMS through multi-dimensional analyses including chronic active lesions, and predict functional outcomes especially in physical and neurocognitive domains. These results are clinically translational and the new measures and techniques can help improve the evaluation and management of both MS and similar diseases

Identification of the presence of ischaemic stroke lesions by means of texture analysis on brain magnetic resonance images

Study funding This work was funded by the Row Fogo Charitable Trust (MVH, VGC) grant no. BRO-D.FID3668413, and the Wellcome Trust (patient recruitment, scanning, primary study Ref No. 088134/Z/09). The study was conducted independently of the funders who do not hold the data and did not participate in the study design or analyses. The Lothian Birth Cohort 1936 is funded by Age UK (Disconnected Mind grant) and the Medical Research Council (MRC; MR/M01311/1, G1001245, 82800), and the latter supported BSA. IJD was supported by the Centre for Cognitive Ageing and Cognitive Epidemiology, which is funded by the MRC and the Biotechnology and Biological Sciences Research Council (MR/K026992/1). David Moratal acknowledges financial support from the Spanish Ministerio de Economía y Competitividad (MINECO) and FEDER funds under Grant BFU2015-64380-C2-2-R, and from the Conselleria d'Educació, Investigació, Cultura i Esport, Generalitat Valenciana (grants AEST/2017/013 and AEST/2018/021). Rafael Ortiz-Ramón was supported by grant ACIF/2015/078 and grant BEFPI/2017/004 from the Conselleria d’Educació, Investigació, Cultura i Esport of the Valencian Community (Spain).Peer reviewedPublisher PD