# Comparative Study of Anatomical and Learned Features in AI Models for Structural Brain MRI

arXiv: https://arxiv.org/abs/2609.06807 · HTML: https://mlsanity.com/paper/2609.06807/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 48 references that are in the map.
- First posted on arXiv 6 Sep 2026.

## Builds on (most cited first, 22 of 22)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
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- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
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- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
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- [FastSurfer -- A fast and accurate deep learning based neuroimaging pipeline](https://mlsanity.com/paper/1910.03866/) (2019)
- [The University of California San Francisco Preoperative Diffuse Glioma MRI (UCSF-PDGM) Dataset](https://mlsanity.com/paper/2109.00356/) (2021)
- [BrainSegFounder: Towards 3D Foundation Models for Neuroimage Segmentation](https://mlsanity.com/paper/2406.10395/) (2024)
- [MeLo: Low-rank Adaptation is Better than Fine-tuning for Medical Image Diagnosis](https://mlsanity.com/paper/2311.08236/) (2023)
- [Predicting Alzheimer's disease: a neuroimaging study with 3D convolutional neural networks](https://mlsanity.com/paper/1502.02506/) (2015)
- [3D Foundation Model for Generalizable Disease Detection in Head Computed Tomography](https://mlsanity.com/paper/2502.02779/) (2025)
- [A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections](https://mlsanity.com/paper/2105.11239/) (2021)

## Abstract (arXiv)

In this work, we comprehensively evaluate three popular feature-extraction paradigms in AI-based neuroimaging modeling: (1) computation of anatomical surfaces and volumes, (2) supervised learning with convolutional neural networks (CNNs), and (3) unsupervised pretraining of vision transformer (ViT) foundation models, followed by supervised finetuning. Our study is based on 18 publicly available datasets containing 3D structural T1-weighted MRI scans from approximately 80,000 participants across seven distinct clinical tasks. We observe that a linear model based on anatomical features matches the diagnostic performance of complex nonlinear features learned by sophisticated AI frameworks, including foundation models trained on thousands of scans. Conversely, CNNs and pretrained ViTs learn features that implicitly capture relevant anatomical information, bypassing the need for explicit feature extraction. Building upon these insights, we propose Anatomy Segmentation Pretraining (ASP), a novel method to incorporate anatomical information during foundation-model pretraining, which outperforms existing models in biological age estimation.