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Performing quality control to detect image artifacts and data-processing errors is crucial in structural magnetic resonance imaging, especially in developmental studies. Currently, many studies rely on visual inspection by trained raters for quality control. The subjectivity of these manual procedures lessens comparability between studies, and with growing study sizes quality control is increasingly time consuming. In addition, both inter-rater as well as intra-rater variability of manual quality control is high and may lead to inclusion of poor quality scans and exclusion of scans of usable quality. In the current study we present the Qoala-T tool, which is an easy and free to use supervised-learning model to reduce rater bias and misclassification in manual quality control procedures using FreeSurfer-processed scans. First, we manually rated quality of N = 784 FreeSurfer-processed T1-weighted scans acquired in three different waves in a longitudinal study. Different supervised-learning models were then compared to predict manual quality ratings using FreeSurfer segmented output data. Results show that the Qoala-T tool using random forests is able to predict scan quality with both high sensitivity and specificity (mean area under the curve (AUC) = 0.98). In addition, the Qoala-T tool was also able to adequately predict the quality of two novel unseen datasets (total N = 872). Finally, analyses of age effects showed that younger participants were more likely to have lower scan quality, underlining that scan quality might confound findings attributed to age effects. These outcomes indicate that this procedure could further help to reduce variability related to manual quality control, thereby benefiting the comparability of data quality between studies. [Display omitted] •Variability of manual quality control procedures reduces comparability among studies.•We introduce Qoala-T to automatically assess quality of FreeSurfer-processed scans.•Scan quality of novel datasets was adequately predicted using the Qoala-T tool.•In three different datasets younger age was associated with lower scan quality.•Qoala-T is publicly available and easy-to-use as an add-on to manual QC.

Objectives Subjective cognitive decline (SCD) and amnestic mild cognitive impairment (aMCI) are known as the preclinical and early stage of Alzheimer's disease (AD). The dorsal attention network (DAN) is mainly responsible for the “top‐down” attention process. However, previous studies mainly focused on single functional modality and limited structure. This study aimed to investigate the multimodal alterations of DAN in SCD and aMCI to assess their diagnostic value in preclinical and early‐stage AD. Methods Resting‐state functional magnetic resonance imaging (MRI) was carried out to measure the fractional amplitude of low‐frequency fluctuation (fALFF), regional homogeneity (ReHo), and functional connectivity (FC). Structural MRI was used to calculate the gray matter volume (GMV) and cortical thickness. Moreover, receiver‐operating characteristic (ROC) analysis was used to distinguish these alterations in SCD and aMCI. Results The SCD and aMCI groups showed both decreased ReHo in the right middle temporal gyrus (MTG) and decreased GMV compared to healthy controls (HCs). Especially in the SCD group, there were increased fALFF and increased ReHo in the left inferior occipital gyrus (IOG), decreased fALFF and increased FC in the left inferior parietal lobule (IPL), and reduced cortical thickness in the right inferior temporal gyrus (ITG). Furthermore, functional and structural alterations in the SCD and aMCI groups were closely related to episodic memory (EM), executive function (EF), and information processing speed (IPS). The combination of multiple indicators of DAN had a high accuracy in differentiating clinical stages. Conclusions Our current study demonstrated functional and structural alterations of DAN in SCD and aMCI, especially in the MTG, IPL, and SPL. Furthermore, cognitive performance was closely related to these significant alterations. Our study further suggested that the combined multiple indicators of DAN could be acted as the latent neuroimaging markers of preclinical and early‐stage AD for their high diagnostic value. Our current study demonstrated obviously functional and structural alterations of DAN in SCD and aMCI. We found that the abnormalities of the functional alterations were especially located in the IPL, IOG, and MTG, whereas structural alterations were mainly in the SPL and ITG. Furthermore, cognitive performance was closely related to these significant alterations. Our study further suggested that the combined multiple indicators of DAN could be acted as the latent neuroimaging markers of preclinical and early‐stage AD for their high diagnostic value.

The human brain is an extremely complex system in which neurons, clusters of neurons, or regions are connected to form a complex network. With the development of neuroimaging techniques, magnetic resonance imaging (MRI)-based brain networks play a key role in our understanding of the intricate architecture of human brain. Among them, the structural MRI-based brain morphological network approach has attracted increasing attention due to the advantages in data acquisition, image quality, and in revealing the structural organizing principles intrinsic to the brain. This review is to summarize the methodology and related applications of individual-level morphological networks. There have been a growing number of studies related to brain morphological similarity networks. Conventional morphological networks are intersubject covariance networks constructed using a certain morphological indicator of a group of subjects; individual-level morphological networks, on the other hand, measure the morphological similarity between brain regions for individual brains and can reflect the morphological information of single subjects. In recent years, individual morphological networks have demonstrated significant worth in exploring the topological changes of the human brain under both normal and disease conditions. Such studies provided novel perspectives for understanding human brain development and exploring the pathological mechanisms of neuropsychiatric disorders. This paper mainly focuses on the studies of brain morphological networks at the individual level, introduces several ways for network construction, reviews representative work in this field, and finally points out current problems and future directions.

Brain structural morphology varies over the aging trajectory, and the prediction of a person’s age using brain morphological features can help the detection of an abnormal aging process. Neuroimaging-based brain age is widely used to quantify an individual’s brain health as deviation from a normative brain aging trajectory. Machine learning approaches are expanding the potential for accurate brain age prediction but are challenging due to the great variety of machine learning algorithms. Here, we aimed to compare the performance of the machine learning models used to estimate brain age using brain morphological measures derived from structural magnetic resonance imaging scans. We evaluated 27 machine learning models, applied to three independent datasets from the Human Connectome Project (HCP, n = 1113, age range 22–37), the Cambridge Centre for Ageing and Neuroscience (Cam-CAN, n = 601, age range 18–88), and the Information eXtraction from Images (IXI, n = 567, age range 19–86). Performance was assessed within each sample using cross-validation and an unseen test set. The models achieved mean absolute errors of 2.75–3.12, 7.08–10.50, and 8.04–9.86 years, as well as Pearson’s correlation coefficients of 0.11–0.42, 0.64–0.85, and 0.63–0.79 between predicted brain age and chronological age for the HCP, Cam-CAN, and IXI samples, respectively. We found a substantial difference in performance between models trained on the same data type, indicating that the choice of model yields considerable variation in brain-predicted age. Furthermore, in three datasets, regularized linear regression algorithms achieved similar performance to nonlinear and ensemble algorithms. Our results suggest that regularized linear algorithms are as effective as nonlinear and ensemble algorithms for brain age prediction, while significantly reducing computational costs. Our findings can serve as a starting point and quantitative reference for future efforts at improving brain age prediction using machine learning models applied to brain morphometric data.

Schizophrenia (SZ) and autism spectrum disorder (ASD) sharing overlapping symptoms have a long history of diagnostic confusion. It is unclear what their differences at a brain level are. Here, we propose a multimodality fusion classification approach to investigate their divergence in brain function and structure. Using brain functional network connectivity (FNC) calculated from resting‐state fMRI data and gray matter volume (GMV) estimated from sMRI data, we classify the two disorders using the main data (335 SZ and 380 ASD patients) via an unbiased 10‐fold cross‐validation pipeline, and also validate the classification generalization ability on an independent cohort (120 SZ and 349 ASD patients). The classification accuracy reached up to 83.08% for the testing data and 72.10% for the independent data, significantly better than the results from using the single‐modality features. The discriminative FNCs that were automatically selected primarily involved the sub‐cortical, default mode, and visual domains. Interestingly, all discriminative FNCs relating to the default mode network showed an intermediate strength in healthy controls (HCs) between SZ and ASD patients. Their GMV differences were mainly driven by the frontal gyrus, temporal gyrus, and insula. Regarding these regions, the mean GMV of HC fell intermediate between that of SZ and ASD, and ASD showed the highest GMV. The middle frontal gyrus was associated with both functional and structural differences. In summary, our work reveals the unique neuroimaging characteristics of SZ and ASD that can achieve high and generalizable classification accuracy, supporting their potential as disorder‐specific neural substrates of the two entwined disorders. Our study aims to disclose differences between schizophrenia (SZ) and autism spectrum disorder (ASD) in both brain functional connectivity and gray matter. Instead of using statistical analyses, we propose a novel fusion classification method to identify the most discriminative multimodal features that reflect their differences. Our work reveals the unique neuroimaging characteristics of SZ and ASD that can achieve high and generalizable classification accuracy, supporting their potential as disorder‐specific neural substrates of the two entwined disorders.

In this paper, we present a multi-region ensemble classifier approach (MRECA) using a cognitive ensemble of classifiers for accurate identification of attention-deficit/hyperactivity disorder (ADHD) subjects. This approach is developed using the features extracted from the structural MRIs of three different developing brain regions, viz., the amygdala, caudate, and hippocampus. For this study, the structural magnetic resonance imaging (sMRI) data provided by the ADHD-200 consortium has been used to identify the following three classes of ADHD, viz., ADHD-combined, ADHD-inattentive, and the TDC (typically developing control). From the sMRIs of the amygdala, caudate, and hippocampus regions of the brain from the ADHD-200 data, multiple feature sets were obtained using a feature-selecting genetic algorithm (FSGA), in a wraparound approach using an extreme learning machine (ELM) basic classifier. An improved crossover operator for the FSGA has been developed for obtaining higher accuracies compared with other existing crossover operators. From the multiple feature sets and the corresponding ELM classifiers, a classifier-selecting genetic algorithm (CSGA) has been developed to identify the top performing feature sets and their ELM classifiers. These classifiers are then combined using a risk-sensitive hinge loss function to form a risk-sensitive cognitive ensemble classifier resulting in a simultaneous multiclass classification of ADHD with higher accuracies. Performance evaluation of the multi-region ensemble classifier is presented under the following three scenarios, viz., region-based individual (best) classifier, region-based ensemble classifier, and finally a multiple-region-based ensemble classifier. The study results clearly indicate that the proposed “multi-region ensemble classification approach” (MRECA) achieves a much higher classification accuracy of ADHD data (normally a difficult problem because of the variations in the data) compared with other existing methods.

Parkinson's disease (PD) is a progressive, chronic, and neurodegenerative disorder that is primarily diagnosed by clinical examinations and magnetic resonance imaging (MRI). In this study, we proposed a machine learning based radiomics method to predict PD. Fifty healthy controls (HC) along with 70 PD patients underwent resting-state magnetic resonance imaging (rs-fMRI). For all subjects, we extracted five types of 6664 features, including mean amplitude of low-frequency fluctuation (mALFF), mean regional homogeneity (mReHo), resting-state functional connectivity (RSFC), voxel-mirrored homotopic connectivity (VMHC) and grey matter (GM) volume. After conducting dimension reduction utilizing Least absolute shrinkage and selection operator (LASSO), fifty-three radiomic features including 46 RSFCs, 1 mALFF, 3 mReHos, 1 VMHC, 2 GM volumes and 1 clinical factor were retained. The selected features also indicated the most discriminative regions for PD. We further conducted model fitting procedure for classifying subjects in the training set employing random forest and support volume machine (SVM) to evaluate the performance of the two methods. After cross-validation, both methods achieved 100% accuracy and area under curve (AUC) for distinguishing between PD and HC in the training set. In the testing set, SVM performed better than random forest with the accuracy, true positive rate (TPR) and AUC being 85%, 1 and 0.97, respectively. These findings demonstrate the radiomics technique has the potential to support radiological diagnosis and to achieve high classification accuracy for clinical diagnostic systems for patients with PD.

Abstract Recent neuroanatomical pattern recognition studies have shown some promises for developing an objective neuroimaging-based classification related to schizophrenia. This study explored the feasibility of reliably identifying schizophrenia using single and multimodal multivariate neuroimaging features. Multiple brain measures including regional gray matter (GM) volume, cortical thickness, gyrification, fractional anisotropy (FA), and mean diffusivity (MD) were extracted using fully automated procedures. We used Gradient Boosting Decision Tree to identify the most frequently selected features of each set of neuroanatomical metric and fused multimodal measures. The current classification model was trained and validated based on 98 patients with first-episode schizophrenia (FES) and 106 matched healthy controls (HCs). The classification model was trained and tested in an independent dataset of 54 patients with FES and 48 HCs using imaging data acquired on a different magnetic resonance imaging scanner. Using the most frequently selected features from fused structural and diffusion tensor imaging metrics, a classification accuracy of 75.05% was achieved, which was higher than accuracy derived from a single imaging metric. Most prominent discriminative features included cortical thickness of left transverse temporal gyrus and right parahippocampal gyrus, the FA of left corticospinal tract and right external capsule. In the independent cohort, average accuracy was 76.54%, derived from combined features selected from cortical thickness, gyrification, FA, and MD. These features characterized by GM abnormalities and white matter disruptions have discriminative power with respect to the underlying pathological changes in the brain of individuals having schizophrenia. Our results further highlight the potential advantage of multimodal data fusion for identifying schizophrenia.

In this paper, we investigate the use of Non-Negative Matrix Factorization (NNMF) for the analysis of structural neuroimaging data. The goal is to identify the brain regions that co-vary across individuals in a consistent way, hence potentially being part of underlying brain networks or otherwise influenced by underlying common mechanisms such as genetics and pathologies. NNMF offers a directly data-driven way of extracting relatively localized co-varying structural regions, thereby transcending limitations of Principal Component Analysis (PCA), Independent Component Analysis (ICA) and other related methods that tend to produce dispersed components of positive and negative loadings. In particular, leveraging upon the well known ability of NNMF to produce parts-based representations of image data, we derive decompositions that partition the brain into regions that vary in consistent ways across individuals. Importantly, these decompositions achieve dimensionality reduction via highly interpretable ways and generalize well to new data as shown via split-sample experiments. We empirically validate NNMF in two data sets: i) a Diffusion Tensor (DT) mouse brain development study, and ii) a structural Magnetic Resonance (sMR) study of human brain aging. We demonstrate the ability of NNMF to produce sparse parts-based representations of the data at various resolutions. These representations seem to follow what we know about the underlying functional organization of the brain and also capture some pathological processes. Moreover, we show that these low dimensional representations favorably compare to descriptions obtained with more commonly used matrix factorization methods like PCA and ICA. •Non-Negative Matrix Factorization for the analysis of structural neuroimaging data•NNMF identifies regions that co-vary across individuals in a consistent way.•NNMF components align well with anatomical structures and follow functional units.•Comprehensive comparison between PCA, ICA and NNMF.•NNMF enjoys increased specificity and generalizability compared to PCA and ICA.

•Single-subject morphological brain networks differed between males and females.•Single-subject morphological brain networks were predictive of individual performance in cognition and motor domains.•Single-subject morphological brain networks provided fingerprints for individual identification.•Different types of single-subject morphological brain networks were distinctively related to genetic, cytoarchitectonic and chemoarchitectonic factors. Although single-subject morphological brain networks provide an important way for human connectome studies, their roles and origins are poorly understood. Combining cross-sectional and repeated structural magnetic resonance imaging scans from adults, children and twins with behavioral and cognitive measures and brain-wide transcriptomic, cytoarchitectonic and chemoarchitectonic data, this study examined phenotypic associations and neurobiological substrates of single-subject morphological brain networks. We found that single-subject morphological brain networks explained inter-individual variance and predicted individual outcomes in Motor and Cognition domains, and distinguished individuals from each other. The performance can be further improved by integrating different morphological indices for network construction. Low-moderate heritability was observed for single-subject morphological brain networks with the highest heritability for sulcal depth-derived networks and higher heritability for inter-module connections. Furthermore, differential roles of genetic, cytoarchitectonic and chemoarchitectonic factors were observed for single-subject morphological brain networks. Cortical thickness-derived networks were related to the three factors with contributions from genes enriched in membrane and transport related functions, genes preferentially located in supragranular and granular layers, overall thickness in the molecular layer and thickness of wall in the infragranular layers, and metabotropic glutamate receptor 5 and dopamine transporter; fractal dimension-, gyrification index- and sulcal depth-derived networks were only associated with the chemoarchitectonic factor with contributions from different sets of neurotransmitter receptors. Most results were reproducible across different parcellation schemes and datasets. Altogether, this study demonstrates phenotypic associations and neurobiological substrates of single-subject morphological brain networks, which provide intermediate endophenotypes to link molecular and cellular architecture and behavior and cognition.