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Roberto Bellotti

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6 papers

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YNICL Journal 2022 Journal Article

Multi-site harmonization of MRI data uncovers machine-learning discrimination capability in barely separable populations: An example from the ABIDE dataset

Sara Saponaro
Alessia Giuliano
Roberto Bellotti
Angela Lombardi
Sabina Tangaro
Piernicola Oliva
Sara Calderoni
Alessandra Retico

Machine Learning (ML) techniques have been widely used in Neuroimaging studies of Autism Spectrum Disorders (ASD) both to identify possible brain alterations related to this condition and to evaluate the predictive power of brain imaging modalities. The collection and public sharing of large imaging samples has favored an even greater diffusion of the use of ML-based analyses. However, multi-center data collections may suffer the batch effect, which, especially in case of Magnetic Resonance Imaging (MRI) studies, should be curated to avoid confounding effects for ML classifiers and masking biases. This is particularly important in the study of barely separable populations according to MRI data, such as subjects with ASD compared to controls with typical development (TD). Here, we show how the implementation of a harmo- nization protocol on brain structural features unlocks the case-control ML separation capability in the analysis of a multi-center MRI dataset. This effect is demonstrated on the ABIDE data collection, involving subjects encompassing a wide age range. After data harmonization, the overall ASD vs. TD discrimination capability by a Random Forest (RF) classifier improves from a very low performance (AUC = 0.58 ± 0.04) to a still low, but reasonably significant AUC = 0.67 ± 0.03. The performances of the RF classifier have been evaluated also in the age-specific subgroups of children, adolescents and adults, obtaining AUC = 0.62 ± 0.02, AUC = 0.65 ± 0.03 and AUC = 0.69 ± 0.06, respectively. Specific and consistent patterns of anatomical differences related to the ASD condition have been identified for the three different age subgroups.

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YNIMG Journal 2021 Journal Article

Predicting brain age with complex networks: From adolescence to adulthood

Loredana Bellantuono
Luca Marzano
Marianna La Rocca
Dominique Duncan
Angela Lombardi
Tommaso Maggipinto
Alfonso Monaco
Sabina Tangaro

In recent years, several studies have demonstrated that machine learning and deep learning systems can be very useful to accurately predict brain age. In this work, we propose a novel approach based on complex networks using 1016 T1-weighted MRI brain scans (in the age range 7-64years). We introduce a structural connectivity model of the human brain: MRI scans are divided in rectangular boxes and Pearson's correlation is measured among them in order to obtain a complex network model. Brain connectivity is then characterized through few and easy-to-interpret centrality measures; finally, brain age is predicted by feeding a compact deep neural network. The proposed approach is accurate, robust and computationally efficient, despite the large and heterogeneous dataset used. Age prediction accuracy, in terms of correlation between predicted and actual age r=0.89and Mean Absolute Error MAE =2.19years, compares favorably with results from state-of-the-art approaches. On an independent test set including 262 subjects, whose scans were acquired with different scanners and protocols we found MAE =2.52. The only imaging analysis steps required in the proposed framework are brain extraction and linear registration, hence robust results are obtained with a low computational cost. In addition, the network model provides a novel insight on aging patterns within the brain and specific information about anatomical districts displaying relevant changes with aging.

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YNIMG Journal 2019 Journal Article

Modelling cognitive loads in schizophrenia by means of new functional dynamic indexes

Angela Lombardi
Cataldo Guaragnella
Nicola Amoroso
Alfonso Monaco
Leonardo Fazio
Paolo Taurisano
Giulio Pergola
Giuseppe Blasi

Functional connectivity analysis techniques have broadly applied to capture phenomenological aspects of the brain, e. g. , by identifying characteristic network topologies for healthy and disease-affected populations, by highlighting several areas important for the global efficiency of the brain during some cognitive processing and at rest. However, most of the known methods for quantifying functional coupling between fMRI time series are focused on linear correlation metrics. In this work, we propose a multidimensional framework to extract multiple descriptors of the dynamic interaction among BOLD signals in their phase space. A set of metrics is extracted from the cross recurrence plots of each couple of signals to form a multilayer connectivity matrix in which each layer is related to a specific complex dynamic phenomenon. The proposed framework is used to characterize functional abnormalities during a working memory task in patients with schizophrenia. Some topological descriptors are then extracted from both multilayer connectivity matrices and the most used Pearson-based connectivity networks to perform a binary classification task of normal controls and patients. The results show that the proposed connectivity model outperforms the statistical correlation-based connectivity in accuracy, sensitivity and specificity. Moreover, the statistical analysis of the selected features highlights that several dynamic metrics could better identify disease-related dynamic states in brain activity than the statistical correlation among physiological signals.

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YNIMG Journal 2016 Journal Article

Integrating longitudinal information in hippocampal volume measurements for the early detection of Alzheimer's disease

Andrea Chincarini
Francesco Sensi
Luca Rei
Gianluca Gemme
Sandro Squarcia
Renata Longo
Francesco Brun
Sabina Tangaro

Background Structural MRI measures for monitoring Alzheimer's Disease (AD) progression are becoming instrumental in the clinical practice, and more so in the context of longitudinal studies. This investigation addresses the impact of four image analysis approaches on the longitudinal performance of the hippocampal volume. Methods We present a hippocampal segmentation algorithm and validate it on a gold-standard manual tracing database. We segmented 460 subjects from ADNI, each subject having been scanned twice at baseline, 12-month and 24month follow-up scan (1. 5T, T1 MRI). We used the bilateral hippocampal volume v and its variation, measured as the annualized volume change Λ= δv/year(mm 3/y). Four processing approaches with different complexity are compared to maximize the longitudinal information, and they are tested for cohort discrimination ability. Reference cohorts are Controls vs. Alzheimer's Disease (CTRL/AD) and CTRL vs. Mild Cognitive Impairment who subsequently progressed to AD dementia (CTRL/MCI-co). We discuss the conditions on v and the added value of Λ in discriminating subjects. Results The age-corrected bilateral annualized atrophy rate (%/year) were: −1. 6 (0. 6) for CTRL, −2. 2 (1. 0) for MCI-nc, −3. 2 (1. 2) for MCI-co and −4. 0 (1. 5) for AD. Combined (v, Λ) discrimination ability gave an Area under the ROC curve (auc)=0. 93 for CTRL vs AD and auc =0. 88 for CTRL vs MCI-co. Conclusions Longitudinal volume measurements can provide meaningful clinical insight and added value with respect to the baseline provided the analysis procedure embeds the longitudinal information.

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YNIMG Journal 2015 Journal Article

Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: The CADDementia challenge

Esther E. Bron
Marion Smits
Wiesje M. van der Flier
Hugo Vrenken
Frederik Barkhof
Philip Scheltens
Janne M. Papma
Rebecca M.E. Steketee

Algorithms for computer-aided diagnosis of dementia based on structural MRI have demonstrated high performance in the literature, but are difficult to compare as different data sets and methodology were used for evaluation. In addition, it is unclear how the algorithms would perform on previously unseen data, and thus, how they would perform in clinical practice when there is no real opportunity to adapt the algorithm to the data at hand. To address these comparability, generalizability and clinical applicability issues, we organized a grand challenge that aimed to objectively compare algorithms based on a clinically representative multi-center data set. Using clinical practice as the starting point, the goal was to reproduce the clinical diagnosis. Therefore, we evaluated algorithms for multi-class classification of three diagnostic groups: patients with probable Alzheimer's disease, patients with mild cognitive impairment and healthy controls. The diagnosis based on clinical criteria was used as reference standard, as it was the best available reference despite its known limitations. For evaluation, a previously unseen test set was used consisting of 354 T1-weighted MRI scans with the diagnoses blinded. Fifteen research teams participated with a total of 29 algorithms. The algorithms were trained on a small training set (n=30) and optionally on data from other sources (e. g. , the Alzheimer's Disease Neuroimaging Initiative, the Australian Imaging Biomarkers and Lifestyle flagship study of aging). The best performing algorithm yielded an accuracy of 63. 0% and an area under the receiver-operating-characteristic curve (AUC) of 78. 8%. In general, the best performances were achieved using feature extraction based on voxel-based morphometry or a combination of features that included volume, cortical thickness, shape and intensity. The challenge is open for new submissions via the web-based framework: http: //caddementia. grand-challenge. org.

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YNIMG Journal 2011 Journal Article

Local MRI analysis approach in the diagnosis of early and prodromal Alzheimer's disease

Andrea Chincarini
Paolo Bosco
Piero Calvini
Gianluca Gemme
Mario Esposito
Chiara Olivieri
Luca Rei
Sandro Squarcia

Background Medial temporal lobe (MTL) atrophy is one of the key biomarkers to detect early neurodegenerative changes in the course of Alzheimer's disease (AD). There is active research aimed at identifying automated methodologies able to extract accurate classification indexes from T1-weighted magnetic resonance images (MRI). Such indexes should be fit for identifying AD patients as early as possible. Subjects A reference group composed of 144AD patients and 189 age-matched controls was used to train and test the procedure. It was then applied on a study group composed of 302 MCI subjects, 136 having progressed to clinically probable AD (MCI-converters) and 166 having remained stable or recovered to normal condition after a 24month follow-up (MCI-non converters). All subjects came from the ADNI database. Methods We sampled the brain with 7 relatively small volumes, mainly centered on the MTL, and 2 control regions. These volumes were filtered to give intensity and textural MRI-based features. Each filtered region was analyzed with a Random Forest (RF) classifier to extract relevant features, which were subsequently processed with a Support Vector Machine (SVM) classifier. Once a prediction model was trained and tested on the reference group, it was used to compute a classification index (CI) on the MCI cohort and to assess its accuracy in predicting AD conversion in MCI patients. The performance of the classification based on the features extracted by the whole 9 volumes is compared with that derived from each single volume. All experiments were performed using a bootstrap sampling estimation, and classifier performance was cross-validated with a 20-fold paradigm. Results We identified a restricted set of image features correlated with the conversion to AD. It is shown that most information originate from a small subset of the total available features, and that it is enough to give a reliable assessment. We found multiple, highly localized image-based features which alone are responsible for the overall clinical diagnosis and prognosis. The classification index is able to discriminate Controls from AD with an Area Under Curve (AUC)=0. 97 (sensitivity ≃89% at specificity ≃94%) and Controls from MCI-converters with an AUC=0. 92 (sensitivity ≃89% at specificity ≃80%). MCI-converters are separated from MCI-non converters with AUC=0. 74(sensitivity ≃72% at specificity ≃65%). Findings The present automated MRI-based technique revealed a strong relationship between highly localized baseline-MRI features and the baseline clinical assessment. In addition, the classification index was also used to predict the probability of AD conversion within a time frame of two years. The definition of a single index combining local analysis of several regions can be useful to detect AD neurodegeneration in a typical MCI population.

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