ACAM-J-MARS: Multi-Atlas Riemannian Spectral Representations for Decoding Advanced Meditation States from fMRI

Introduction: Jhana advanced concentrative absorption meditation (ACAM-J) involves profound changes in consciousness, making its neural correlates important for understanding consciousness and well-being. Prior neuroimaging has relied on univariate, group-level contrasts, leaving open whether ACAM-J carries distributed neural signatures decodable from individual scans. This study evaluates whether fMRI-derived regional homogeneity (ReHo) can classify ACAM-J using machine learning. Methods: We analysed 7T fMRI data from 20 advanced meditators who progressed through their standard ACAM-J sequence and two matched control tasks, plus intensive data from one case-study participant held out for final evaluation. ReHo maps were computed per segment and parcellated into 498 regions spanning cortex, subcortex, brainstem, and cerebellum. Within subject-wise stratified cross-validation, feature ranking, recursive feature elimination, and class balancing were applied to training data only; six classifier families were fitted, and the top three per contrast were combined by probability averaging. Results: Across 19 binary comparisons, the ensemble reached an overall average accuracy of 65.87% before and 66.82% after regressing out phenomenology-related variance, with an average Cohen's \k{appa} of 0.2443. Discrimination was strongest for the most separated states (ACAM-J1 vs ACAM-J6, 74.33% accuracy, \k{appa} = 0.5158), while adjacent states were harder to separate. Prefrontal and anterior cingulate areas contributed most to model decisions. Conclusion: ReHo patterns measured at 7T carry information distinguishing ACAM-J from control states and, more modestly, from one another, supporting the feasibility of multivariate decoding of advanced meditation and informing future work on its mechanisms and neuromodulation.

Foundation models pre-trained on large-scale fMRI datasets have shown strong downstream performance, but at substantial data and computation cost. To investigate how much fMRI-specific pre-training is actually needed for such performance, we introduce FReD, which derives fMRI representations from a frozen Deep Compression AutoEncoder (DCAE) pre-trained exclusively on natural images and pairs them with a task specific readout. For trait prediction, FReD summarizes frame-wise representations by their temporal mean and log-standard deviation and applies linear probing, with late fusion across two normalization schemes. For state prediction, it represents each frame as a single token and models temporal dependencies with a shallow Transformer. Across four resting-state datasets spanning six trait-prediction targets, linear probes on frozen DCAE features generally outperform those on fMRI foundation model representations and remain competitive with fully fine-tuned fMRI foundation models. On three task-fMRI state-prediction tasks, a temporal readout on DCAE features performs comparably to the strongest foundation models evaluated. A Gaussian injection analysis further shows that localized signal changes are recovered more accurately from the frozen DCAE features than from the evaluated foundation-model representations. Together, these results show that strong performance on current fMRI benchmarks is possible without fMRI-specific representation pre-training, making frozen natural-image features as a useful baseline for assessing its added value.

Functional connectivity (FC) derived from resting-state fMRI is widely used to characterize large-scale brain network alterations in neurological and psychiatric disorders. However, FC construction critically depends on the choice of brain atlas, and different parcellations may emphasize distinct organizational features, leading to heterogeneous and sometimes inconsistent representations. Existing multi-atlas approaches partially alleviate this issue but often fuse atlas-derived features or predictions at a relatively shallow level, while single-atlas disentanglement methods do not explicitly address cross-atlas heterogeneity. We propose Multi-Atlas Disentangled Connectivity LEarning (MADCLE), a multi-branch representation learning framework that jointly encodes FC matrices derived from different brain atlases. Rather than introducing a single explicitly shared latent variable across parcellations, MADCLE learns atlas-wise disease-related representations and encourages them to be cross-atlas consistent through distributional alignment. Meanwhile, covariate-related and atlas-dependent residual factors are modeled separately using covariate similarity supervision, atlas-specific reconstruction, and decorrelation constraints, thereby reducing the leakage of non-disease and parcellation-dependent information into the disease-related embeddings. Experiments on the ADNI and ADHD-200 datasets suggest that MADCLE achieves competitive or improved performance compared with single-atlas baselines, multi-atlas GNN/Transformer models, and recent multi-atlas consistency frameworks. These results support the potential value of structured disentanglement for FC-based disorder identification under heterogeneous parcellation schemes.