arXiv subjects

Cesar Kadir Torrico Villanueva

Publications and source records attributed to Cesar Kadir Torrico Villanueva.

5 recordsLinked to original sources

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.

cs.CV↗

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↗

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↗

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↗