Data-driven haemodynamic response function extraction using Fourier-wavelet regularised deconvolution

Background: We present a simple, data-driven method to extract haemodynamic response functions (HRF) from functional magnetic resonance imaging (fMRI) time series, based on the Fourier-wavelet regularised deconvolution (ForWaRD) technique. HRF data are required for many fMRI applications, such as defining region-specific HRFs, effciently representing a general HRF, or comparing subject-specific HRFs. Results: ForWaRD is applied to fMRI time signals, after removing low-frequency trends by a wavelet-based method, and the output of ForWaRD is a time series of volumes, containing the HRF in each voxel. Compared to more complex methods, this extraction algorithm requires few assumptions (separability of signal and noise in the frequency and wavelet domains and the general linear model) and it is fast (HRF extraction from a single fMRI data set takes about the same time as spatial resampling). The extraction method is tested on simulated event-related activation signals, contaminated with noise from a time series of real MRI images. An application for HRF data is demonstrated in a simple event-related experiment: data are extracted from a region with significant effects of interest in a first time series. A continuous-time HRF is obtained by fitting a nonlinear function to the discrete HRF coeffcients, and is then used to analyse a later time series. Conclusion: With the parameters used in this paper, the extraction method presented here is very robust to changes in signal properties. Comparison of analyses with fitted HRFs and with a canonical HRF shows that a subject-specific, regional HRF significantly improves detection power. Sensitivity and specificity increase not only in the region from which the HRFs are extracted, but also in other regions of interest.

BOLD Noise Assumptions in fMRI.

This paper discusses the assumption of Gaussian noise in the blood-oxygenation-dependent (BOLD) contrast for functional MRI (fMRI). In principle, magnitudes in MRI images follow a Rice distribution. We start by reviewing differences between Rician and Gaussian noise. An analytic expression is derived for the null (resting-state) distribution of the difference between two Rician distributed images. This distribution is shown to be symmetric, and an exact expression for its standard deviation is derived. This distribution can be well approximated by a Gaussian, with very high precision for high SNR, and high precision for lower SNR. Tests on simulated and real MR images show that subtracting the time-series mean in fMRI yields asymmetrically distributed temporal noise. Subtracting a resting-state time series from the first results in symmetric and nearly Gaussian noise. This has important consequences for fMRI analyses using standard statistical tests.Peer Reviewe

BOLD Noise Assumptions in fMRI

This paper discusses the assumption of Gaussian noise in the blood-oxygenation-dependent (BOLD) contrast for functional MRI (fMRI). In principle, magnitudes in MRI images follow a Rice distribution. We start by reviewing differences between Rician and Gaussian noise. An analytic expression is derived for the null (resting-state) distribution of the difference between two Rician distributed images. This distribution is shown to be symmetric, and an exact expression for its standard deviation is derived. This distribution can be well approximated by a Gaussian, with very high precision for high SNR, and high precision for lower SNR. Tests on simulated and real MR images show that subtracting the time-series mean in fMRI yields asymmetrically distributed temporal noise. Subtracting a resting-state time series from the first results in symmetric and nearly Gaussian noise. This has important consequences for fMRI analyses using standard statistical tests

Evaluation of novel data-driven metrics of amyloid β deposition for longitudinal PET studies

PURPOSE: Positron emission tomography (PET) provides in vivo quantification of amyloid-β (Aβ) pathology. Established methods for assessing Aβ burden can be affected by physiological and technical factors. Novel, data-driven metrics have been developed to account for these sources of variability. We aimed to evaluate the performance of four data-driven amyloid PET metrics against conventional techniques, using a common set of criteria. METHODS: Three cohorts were used for evaluation: Insight 46 (N=464, [18F]florbetapir), AIBL (N=277, [18F]flutemetamol), and an independent test-retest data (N=10, [18F]flutemetamol). Established metrics of amyloid tracer uptake included the Centiloid (CL) and where dynamic data was available, the non-displaceable binding potential (BPND). The four data driven metrics computed were the amyloid load (Aβ load), the Aβ PET pathology accumulation index (Aβ index), the Centiloid derived from non-negative matrix factorisation (CLNMF), and the amyloid pattern similarity score (AMPSS). These metrics were evaluated using reliability and repeatability in test-retest data, associations with BPND and CL, and sample size estimates to detect a 25% slowing in Aβ accumulation. RESULTS: All metrics showed good reliability. Aβ load, Aβ index and CLNMF were strong associated with the BPND. The associations with CL suggests that cross-sectional measures of CLNMF, Aβ index and Aβ load are robust across studies. Sample size estimates for secondary prevention trial scenarios were the lowest for CLNMF and Aβ load compared to the CL. CONCLUSION: Among the novel data-driven metrics evaluated, the Aβ load, the Aβ index and the CLNMF can provide comparable performance to more established quantification methods of Aβ PET tracer uptake. The CLNMF and Aβ load could offer a more precise alternative to CL, although further studies in larger cohorts should be conducted

Eigenvector centrality dynamics are related to Alzheimer’s disease pathological changes in non-demented individuals

Amyloid-β accumulation starts in highly connected brain regions and is associated with functional connectivity alterations in the early stages of Alzheimer's disease. This regional vulnerability is related to the high neuronal activity and strong fluctuations typical of these regions. Recently, dynamic functional connectivity was introduced to investigate changes in functional network organization over time. High dynamic functional connectivity variations indicate increased regional flexibility to participate in multiple subnetworks, promoting functional integration. Currently, only a limited number of studies have explored the temporal dynamics of functional connectivity in the pre-dementia stages of Alzheimer's disease. We study the associations between abnormal cerebrospinal fluid amyloid and both static and dynamic properties of functional hubs, using eigenvector centrality, and their relationship with cognitive performance, in 701 non-demented participants from the European Prevention of Alzheimer's Dementia cohort. Voxel-wise eigenvector centrality was computed for the whole functional magnetic resonance imaging time series (static), and within a sliding window (dynamic). Differences in static eigenvector centrality between amyloid positive (A+) and negative (A-) participants and amyloid-tau groups were found in a general linear model. Dynamic eigenvector centrality standard deviation and range were compared between groups within clusters of significant static eigenvector centrality differences, and within 10 canonical resting-state networks. The effect of the interaction between amyloid status and cognitive performance on dynamic eigenvector centrality variability was also evaluated with linear models. Models were corrected for age, sex, and education level. Lower static centrality was found in A+ participants in posterior brain areas including a parietal and an occipital cluster; higher static centrality was found in a medio-frontal cluster. Lower eigenvector centrality variability (standard deviation) occurred in A+ participants in the frontal cluster. The default mode network and the dorsal visual networks of A+ participants had lower dynamic eigenvector centrality variability. Centrality variability in the default mode network and dorsal visual networks were associated with cognitive performance in the A- and A+ groups, with lower variability being observed in A+ participants with good cognitive scores. Our results support the role and timing of eigenvector centrality alterations in very early stages of Alzheimer's disease and show that centrality variability over time adds relevant information on the dynamic patterns that cause static eigenvector centrality alterations. We propose that dynamic eigenvector centrality is an early biomarker of the interplay between early Alzheimer's disease pathology and cognitive decline

Spatial-Temporal Patterns of Amyloid-β Accumulation: A Subtype and Stage Inference Model Analysis

BACKGROUND AND OBJECTIVES: Currently, amyloid-β (Aβ) staging models assume a single spatial-temporal progression of amyloid accumulation. We assessed evidence for Aβ accumulation subtypes by applying the data-driven Subtype and Stage Inference (SuStaIn) model to amyloid-PET data. METHODS: Amyloid-PET data of 3010 subjects were pooled from 6 cohorts (ALFA+, EMIF-AD, ABIDE, OASIS, and ADNI). Standardized uptake value ratios (SUVr) were calculated for 17 regions. We applied the SuStaIn algorithm to identify consistent subtypes in the pooled dataset based on the cross-validation information criterion (CVIC) and the most probable subtype/stage classification per scan. The effect of demographics and risk factors on subtype assignment was assessed using multinomial logistic regression. RESULTS: Participants were mostly cognitively unimpaired (N=1890, 62.8%), had a mean age of 68.72 (SD=9.1), 42.1% was APOE-ε4 carrier, and 51.8% was female. While a one-subtype model recovered the traditional amyloid accumulation trajectory, SuStaIn identified an optimal of three subtypes, referred to as Frontal, Parietal, and Occipital based on the first regions to show abnormality. Of the 788 (26.2%) with strong subtype assignment (>50% probability), the majority was assigned to Frontal (N=415, 52.5%), followed by Parietal (N=199, 25.3%), and Occipital subtypes (N=175, 22.2%). Significant differences across subtypes included distinct proportions of APOE-ε4 carriers (Frontal:61.8%, Parietal:57.1%, Occipital:49.4%), subjects with dementia (Frontal:19.7%, Parietal:19.1%, Occipital:31.0%) and lower age for the Parietal subtype (Frontal/Occipital:72.1y, Parietal:69.3y). Higher amyloid (Centiloid) and CSF p-tau burden was observed for the Frontal subtype, while Parietal and Occipital did not differ. At follow-up, most subjects (81.1%) maintained baseline subtype assignment and 25.6% progressed to a later stage. DISCUSSION: While a one-trajectory model recovers the established pattern of amyloid accumulation, SuStaIn determined that three subtypes were optimal, showing distinct associations to AD risk factors. Nonetheless, further analyses to determine clinical utility is warranted

Spatial-Temporal Patterns of Amyloid-β Accumulation: A Subtype and Stage Inference Model Analysis

BACKGROUND AND OBJECTIVES: Currently, amyloid-β (Aβ) staging models assume a single spatial-temporal progression of amyloid accumulation. We assessed evidence for Aβ accumulation subtypes by applying the data-driven Subtype and Stage Inference (SuStaIn) model to amyloid-PET data. METHODS: Amyloid-PET data of 3010 subjects were pooled from 6 cohorts (ALFA+, EMIF-AD, ABIDE, OASIS, and ADNI). Standardized uptake value ratios (SUVr) were calculated for 17 regions. We applied the SuStaIn algorithm to identify consistent subtypes in the pooled dataset based on the cross-validation information criterion (CVIC) and the most probable subtype/stage classification per scan. The effect of demographics and risk factors on subtype assignment was assessed using multinomial logistic regression. RESULTS: Participants were mostly cognitively unimpaired (N=1890, 62.8%), had a mean age of 68.72 (SD=9.1), 42.1% was APOE-ε4 carrier, and 51.8% was female. While a one-subtype model recovered the traditional amyloid accumulation trajectory, SuStaIn identified an optimal of three subtypes, referred to as Frontal, Parietal, and Occipital based on the first regions to show abnormality. Of the 788 (26.2%) with strong subtype assignment (>50% probability), the majority was assigned to Frontal (N=415, 52.5%), followed by Parietal (N=199, 25.3%), and Occipital subtypes (N=175, 22.2%). Significant differences across subtypes included distinct proportions of APOE-ε4 carriers (Frontal:61.8%, Parietal:57.1%, Occipital:49.4%), subjects with dementia (Frontal:19.7%, Parietal:19.1%, Occipital:31.0%) and lower age for the Parietal subtype (Frontal/Occipital:72.1y, Parietal:69.3y). Higher amyloid (Centiloid) and CSF p-tau burden was observed for the Frontal subtype, while Parietal and Occipital did not differ. At follow-up, most subjects (81.1%) maintained baseline subtype assignment and 25.6% progressed to a later stage. DISCUSSION: While a one-trajectory model recovers the established pattern of amyloid accumulation, SuStaIn determined that three subtypes were optimal, showing distinct associations to AD risk factors. Nonetheless, further analyses to determine clinical utility is warranted