Quantitative MRI (qMRI) promises better specificity, accuracy, repeatability, and reproducibility relative to its clinically-used qualitative MRI counterpart. Longitudinal reproducibility is particularly important in qMRI. The goal is to reliably quantify tissue properties that may be assessed in longitudinal clinical studies throughout disease progression or during treatment. In this work, we present the initial data release of the quantitative MRI portion of the Courtois project on neural modelling (CNeuroMod), where the brain and cervical spinal cord of six participants were scanned at regular intervals over the course of several years. This first release includes 3 years of data collection and up to 10 sessions per participant using quantitative MRI imaging protocols (T 1 , magnetization transfer (MTR, MTsat), and diffusion). In the brain, T 1 MP2RAGE , fractional anisotropy (FA), mean diffusivity (MD), and radial diffusivity (RD) all exhibited high longitudinal reproducibility (intraclass correlation coefficient – ICC ≃ 1 and within-subject coefficient of variations – wCV < 1%). The spinal cord cross-sectional area (CSA) computed using T2w images and T 1 MTsat exhibited the best longitudinal reproducibility (ICC ≃ 1 and 0.7 respectively, and wCV 2.4% and 6.9%). Results from this work show the level of longitudinal reproducibility that can be expected from qMRI protocols in the brain and spinal cord in the absence of hardware and software upgrades, and could help in the design of future longitudinal clinical studies.

Dense functional magnetic resonance imaging datasets open new avenues to create auto-regressive models of brain activity. Individual idiosyncrasies are obscured by group models, but can be captured by purely individual models given sufficient amounts of training data. In this study, we compared several deep and shallow individual models on the temporal auto-regression of BOLD time-series recorded during a natural video-watching task. The best performing models were then analyzed in terms of their data requirements and scaling, subject specificity, and the space-time structure of their predicted dynamics. We found the Chebnets, a type of graph convolutional neural network, to be best suited for temporal BOLD auto-regression, closely followed by linear models. Chebnets demonstrated an increase in performance with increasing amounts of data, with no complete saturation at 9 h of training data. Good generalization to other kinds of video stimuli and to resting-state data marked the Chebnets’ ability to capture intrinsic brain dynamics rather than only stimulus-specific autocorrelation patterns. Significant subject specificity was found at short prediction time lags. The Chebnets were found to capture lower frequencies at longer prediction time lags, and the spatial correlations in predicted dynamics were found to match traditional functional connectivity networks. Overall, these results demonstrate that large individual functional magnetic resonance imaging (fMRI) datasets can be used to efficiently train purely individual auto-regressive models of brain activity, and that massive amounts of individual data are required to do so. The excellent performance of the Chebnets likely reflects their ability to combine spatial and temporal interactions on large time scales at a low complexity cost. The non-linearities of the models did not appear as a key advantage. In fact, surprisingly, linear versions of the Chebnets appeared to outperform the original non-linear ones. Individual temporal auto-regressive models have the potential to improve the predictability of the BOLD signal. This study is based on a massive, publicly-available dataset, which can serve for future benchmarks of individual auto-regressive modeling.