arXiv subjects

Paul S. Scotti

Publications and source records attributed to Paul S. Scotti.

9 recordsLinked to original sources

arXiv2026

Real-time Reconstruction of Human Visual Perception from fMRI

Real-time closed-loop neurofeedback based on functional magnetic resonance imaging (fMRI) has led to important scientific and clinical advances. However, the sophistication of the analysis methods used in real-time fMRI lags behind the state-of-the-art in fMRI decoding, largely due to computational factors: Most advanced decoding pipelines do not fit within the envelope of real-time processing, where the analysis needs to be conducted in a matter of seconds and without leveraging data acquired later in the session. Here, we present a real-time compatible adaptation of a computationally intensive state-of-the-art pipeline for reconstructing perceived natural images (MindEye2), and we demonstrate that reliable fine-grained decoding is still achievable in this setting. Using RT-Cloud, an open-source, scalable cloud-based platform, we performed a real-time scan where we decoded single-trial visual perception within seconds after an image was shown to the participant. Finally, we use simulated analyses to document the factors driving changes in performance from offline to real-time analysis. This work serves as a proof-of-concept that it is feasible to deploy these powerful fMRI decoding pipelines in real-time analysis, paving the way for their use in brain-computer interfaces for scientific discovery and clinical treatment.

cs.CV↗

arXiv2026

MIRAGE: Robust multi-modal architectures translate fMRI-to-image models from vision to mental imagery

To be useful for downstream applications, vision decoding models that are trained to reconstruct seen images from human brain activity must be able to generalize to internally generated visual representations, i.e., mental images. In an analysis of the recently released NSD-Imagery dataset, we demonstrated that while some modern vision decoders can perform quite well on mental image reconstruction, some fail, and that state-of-the-art (SOTA) performance on seen image reconstruction is no guarantee of SOTA performance on mental image reconstruction. Motivated by these findings, we developed MIRAGE, a method explicitly designed to train on vision datasets and cross-decode mental images from brain activity. MIRAGE employs a linear backbone and multi-modal text and image features as input to a diffusion model. Feature metrics and human raters establish MIRAGE as SOTA for mental image reconstruction on the NSD-Imagery benchmark. With ablation analysis we show that mental image reconstruction works best when decoders use image features with relatively few dimensions and include guidance from text-based and both high- and low-level image-based features. Our work indicates that--given the right architecture--existing large-scale datasets using external stimuli are viable training data for decoding mental images, and warrant optimism about the future success and utility of mental image reconstruction.

q-bio.NC↗

arXiv2026

Scaling Vision Transformers for Functional MRI with Flat Maps

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.

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arXiv2025

Alljoined-1.6M: A Million-Trial EEG-Image Dataset for Evaluating Affordable Brain-Computer Interfaces

We present a new large-scale electroencephalography (EEG) dataset as part of the THINGS initiative, comprising over 1.6 million visual stimulus trials collected from 20 participants, and totaling more than twice the size of the most popular current benchmark dataset, THINGS-EEG2. Crucially, our data was recorded using a 32-channel consumer-grade wet electrode system costing ~$2.2k, around 27x cheaper than research-grade EEG systems typically used in cognitive neuroscience labs. Our work is one of the first open-source, large-scale EEG resource designed to closely reflect the quality of hardware that is practical to deploy in real-world, downstream applications of brain-computer interfaces (BCIs). We aim to explore the specific question of whether deep neural network-based BCI research and semantic decoding methods can be effectively conducted with such affordable systems, filling an important gap in current literature that is extremely relevant for future research. In our analysis, we not only demonstrate that decoding of high-level semantic information from EEG of visualized images is possible at consumer-grade hardware, but also that our data can facilitate effective EEG-to-Image reconstruction even despite significantly lower signal-to-noise ratios. In addition to traditional benchmarks, we also conduct analyses of EEG-to-Image models that demonstrate log-linear decoding performance with increasing data volume on our data, and discuss the trade-offs between hardware cost, signal fidelity, and the scale of data collection efforts in increasing the size and utility of currently available datasets. Our contributions aim to pave the way for large-scale, cost-effective EEG research with widely accessible equipment, and position our dataset as a unique resource for the democratization and development of effective deep neural models of visual cognition.

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arXiv2025

Insights from the Algonauts 2025 Winners

The Algonauts 2025 Challenge just wrapped up a few weeks ago. It is a biennial challenge in computational neuroscience in which teams attempt to build models that predict human brain activity from carefully curated stimuli. Previous editions (2019, 2021, 2023) focused on still images and short videos; the 2025 edition, which concluded last month (late July), pushed the field further by using long, multimodal movies. Teams were tasked with predicting fMRI responses across 1,000 whole-brain parcels across four participants in the dataset who were scanned while watching nearly 80 hours of naturalistic movie stimuli. These recordings came from the CNeuroMod project and included 65 hours of training data, about 55 hours of Friends (seasons 1-6) plus four feature films (The Bourne Supremacy, Hidden Figures, Life, and The Wolf of Wall Street). The remaining data were used for validation: Season 7 of Friends for in-distribution tests, and the final winners for the Challenge were those who could best predict brain activity for six films in their held-out out-of-distribution (OOD) set. The winners were just announced and the top team reports are now publicly available. As members of the MedARC team which placed 4th in the competition, we reflect on the approaches that worked, what they reveal about the current state of brain encoding, and what might come next.

q-bio.NC↗

arXiv2025

Predicting Brain Responses To Natural Movies With Multimodal LLMs

We present MedARC's team solution to the Algonauts 2025 challenge. Our pipeline leveraged rich multimodal representations from various state-of-the-art pretrained models across video (V-JEPA2), speech (Whisper), text (Llama 3.2), vision-text (InternVL3), and vision-text-audio (Qwen2.5-Omni). These features extracted from the models were linearly projected to a latent space, temporally aligned to the fMRI time series, and finally mapped to cortical parcels through a lightweight encoder comprising a shared group head plus subject-specific residual heads. We trained hundreds of model variants across hyperparameter settings, validated them on held-out movies and assembled ensembles targeted to each parcel in each subject. Our final submission achieved a mean Pearson's correlation of 0.2085 on the test split of withheld out-of-distribution movies, placing our team in fourth place for the competition. We further discuss a last-minute optimization that would have raised us to second place. Our results highlight how combining features from models trained in different modalities, using a simple architecture consisting of shared-subject and single-subject components, and conducting comprehensive model selection and ensembling improves generalization of encoding models to novel movie stimuli. All code is available on GitHub.

cs.CV↗

arXiv2025

NSD-Imagery: A benchmark dataset for extending fMRI vision decoding methods to mental imagery

We release NSD-Imagery, a benchmark dataset of human fMRI activity paired with mental images, to complement the existing Natural Scenes Dataset (NSD), a large-scale dataset of fMRI activity paired with seen images that enabled unprecedented improvements in fMRI-to-image reconstruction efforts. Recent models trained on NSD have been evaluated only on seen image reconstruction. Using NSD-Imagery, it is possible to assess how well these models perform on mental image reconstruction. This is a challenging generalization requirement because mental images are encoded in human brain activity with relatively lower signal-to-noise and spatial resolution; however, generalization from seen to mental imagery is critical for real-world applications in medical domains and brain-computer interfaces, where the desired information is always internally generated. We provide benchmarks for a suite of recent NSD-trained open-source visual decoding models (MindEye1, MindEye2, Brain Diffuser, iCNN, Takagi et al.) on NSD-Imagery, and show that the performance of decoding methods on mental images is largely decoupled from performance on vision reconstruction. We further demonstrate that architectural choices significantly impact cross-decoding performance: models employing simple linear decoding architectures and multimodal feature decoding generalize better to mental imagery, while complex architectures tend to overfit visual training data. Our findings indicate that mental imagery datasets are critical for the development of practical applications, and establish NSD-Imagery as a useful resource for better aligning visual decoding methods with this goal.

cs.CV↗

arXiv2024

MindEye2: Shared-Subject Models Enable fMRI-To-Image With 1 Hour of Data

Reconstructions of visual perception from brain activity have improved tremendously, but the practical utility of such methods has been limited. This is because such models are trained independently per subject where each subject requires dozens of hours of expensive fMRI training data to attain high-quality results. The present work showcases high-quality reconstructions using only 1 hour of fMRI training data. We pretrain our model across 7 subjects and then fine-tune on minimal data from a new subject. Our novel functional alignment procedure linearly maps all brain data to a shared-subject latent space, followed by a shared non-linear mapping to CLIP image space. We then map from CLIP space to pixel space by fine-tuning Stable Diffusion XL to accept CLIP latents as inputs instead of text. This approach improves out-of-subject generalization with limited training data and also attains state-of-the-art image retrieval and reconstruction metrics compared to single-subject approaches. MindEye2 demonstrates how accurate reconstructions of perception are possible from a single visit to the MRI facility. All code is available on GitHub.

cs.CV↗

arXiv2023

Reconstructing the Mind's Eye: fMRI-to-Image with Contrastive Learning and Diffusion Priors

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

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