Brain MRI

MRI: Magnetic Resonance Imaging

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12 papers in the last four weeks, up 20% on the four weeks before. 0.1% of all new papers.

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Latest papers 89

Oct 7, 2026cs.CV

Identity-Duplication Auditing in National-Scale Neuroimaging Repositories

National-scale magnetic resonance imaging (MRI) repositories increasingly integrate data from different studies and institutions. However, subject identifiers that are valid only within individual datasets are no longer guaranteed to remain globally unique after aggregation, making it possible for the same subject to be assigned multiple identifiers, which we define as identity duplication. Such duplication can create leakage between training and test data and inflate apparent performance in downstream biomedical studies. Existing methods do not provide an end-to-end, image-based workflow for auditing this problem at repository scale. In this work, we present HAPPEN, a human-in-the-loop pipeline for auditing identity duplication in T1-weighted brain MRI repositories. It combines SHA-256 fingerprinting for exact-duplicate detection with supervised contrastive retrieval of non-identical scans that may originate from the same person. Retrieved pairs are reviewed as candidates in a locally hosted interface rather than automatically classified as duplicates. We deployed the workflow in a 95,129-scan aggregated repository and assessed end-to-end recovery using 54 genetic-reference pairs. Transferability was assessed by locally deploying the same workflow on 22,386 scans at an independent institution without model retraining or image transfer. Deployment in the study repository identified 1,316 exact-duplicate scan groups and 1,275 reviewer-supported near-duplicate subject groups. Of these groups, 56% and 82%, respectively, crossed dataset boundaries. All 54 genetic-reference pairs were recovered. The external team independently completed the full workflow using a locally selected operating threshold and review standard.

Jiheng Li, Michael E. Kim, Trent M. Schwartz +19

HABS-HD · Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA · AI2D Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, PA, USA +2

Neuroimaging Brain MRI

Oct 6, 2026cs.CV

Zero-Shot Brain MRI Inpainting with 2.5D Unconditional Flow Priors

Generative inpainting of brain MRI volumes is essential for synthesizing healthy tissue in pathological regions, improving the accuracy and reliability of automated downstream brain analysis applications such as image registration, brain extraction, and segmentation. However, standard 3D approaches are computationally prohibitive, while efficient 2D slice-wise methods suffer from severe inter-slice discontinuities. Furthermore, traditional models rely on conditional training, requiring task-specific learning of masked inputs. We propose a zero-shot brain MRI inpainting framework utilizing 2.5D unconditional flow priors to capture spatial context along the superior-inferior axis without the overhead of full 3D convolutions. During training, our flow matching model learns the joint distribution of adjacent axial slice triplets, modeling the manifold of healthy brain anatomy while explicitly excluding pathological regions from the loss function. At inference, the model processes the input triplets autoregressively along the depth axis. We employ the Restora-Flow solver to constrain the unconditional prior using the input mask, achieving accurate zero-shot inpainting. Evaluations show our 2.5D strategy resolves the structural discontinuities of 2D baselines, synthesizing plausible healthy tissue while maintaining volumetric consistency across the axial, sagittal, and coronal planes. As a final step, we generate and average an ensemble of multiple stochastic reconstructions to form the final prediction. Quantitative results benchmarked on the official BraTS 2026 Inpainting Challenge validation set demonstrate the effectiveness of our proposed approach, yielding an SSIM of 0.816

\pm

0.112, MSE of 0.007

\pm

0.005, and PSNR of 22.923

\pm

4.343. Code is available at https://github.com/imigraz/brats2026-inpainting.

Arnela Hadzic, Franz Thaler, Simon Johannes Joham +1

Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria

Image Inpainting Medical Image Synthesis Brain MRI

Oct 5, 2026cs.CV

BrainTRACE: Tracing Longitudinal, Multimodal, and Volumetric Evidence in Brain MRI Clinical Reasoning

Brain MRI interpretation is a longitudinal clinical reasoning problem: radiologists compare serial studies, integrate information across MRI sequences, localize findings within volumetric anatomy, and translate this evidence into report-grounded assessments. Existing medical VQA and 3D imaging benchmarks capture important parts of this workflow, but often evaluate brain MRI through isolated images, static volumes, or ungrounded report-style answers, thereby obscuring failures in the evidence chain that support clinical validity. We introduce BrainTRACE, a report-grounded benchmark for evaluating whether vision-language models can trace the evidence structure required for longitudinal brain MRI interpretation. BrainTRACE contains 7,273 scored VQA instances derived from 1,778 longitudinal patients, 7,299 MRI studies, and approximately 29k co-registered 3D MRI sequence volumes. The benchmark is organized by five levels of clinical reasoning, from acquisition recognition to case-level synthesis, and by evidence demands covering longitudinal comparison, report-grounded references, multi-sequence integration, and volumetric spatial evidence. BrainTRACE supports rendered inputs compatible with standard VLM interfaces, a 3D-evidence condition, and a decomposed case-reasoning track that audits six steps in a longitudinal evidence chain. Evaluation of 20 VLM configurations shows that current systems can identify isolated visual cues but rarely compose them into grounded longitudinal interpretations. We release the benchmark specification, evaluation lists, scoring implementation, scoring rubrics, and audit-record format to support reproducible progress in brain MRI VLM evaluation.

Qizhen Lan, Mengchen Fan, Hang Zhang +5

University of Texas Health Science Center at Houston · University of Alabama at Birmingham · University of Pittsburgh +3

VLM Evaluation 3D Medical Imaging Medical VQA Medical Image Grounding Brain MRI

Oct 5, 2026cs.CV

NeuroCBIR: A Fast and Accurate Image Retrieval System for Whole-Brain and Region-Specific MRI

Content-based image retrieval (CBIR) in neuroimaging enables the identification of structurally similar brain scans, supporting diagnosis, prognosis, and treatment planning; however, existing methods are often limited to small datasets, single brain regions, or coarse class labels, thereby restricting their clinical utility and generalizability. Here, we present NeuroCBIR, a framework for fast and flexible retrieval of both whole-brain and region-specific 3D T1w MRI scans. A total of 103 cortical and subcortical regions are extracted to enable both whole-brain and region-level queries. NeuroCBIR leverages latent representations learned by a variational autoencoder (VAE) combined with contrastive learning, producing scan-specific embeddings that capture anatomical patterns. These embeddings were evaluated for subject re-identification, zero-shot age prediction, and zero-shot multi-class pathology stratification. Re-identification performance was high across both whole-brain and brain-region levels (mean average precision across the top-5 retrieved images (mAP@5) >= 98.4%), with robust generalization across datasets and acquisition conditions. While NeuroCBIR is not trained for age prediction or pathology stratification, zero-shot evaluations for these two tasks demonstrate that the embeddings encode meaningful information for downstream tasks. Embedding extraction on a 4-core CPU required approximately 18.7 s per scan, whereas similarity search was effectively instantaneous (less than 0.01 s). NeuroCBIR is publicly available for brain MRI with more than 26,000 precomputed T1w MRI embeddings. It supports reproducible research, region-specific flexibility, and clinically meaningful personalized diagnostic support. The software is available at https://github.com/minnelab/NeuroCBIR.

Felix Nieto-del-Amor, Jingru Fu, J. -Sebastian Muehlboeck +3

Medical Image Representation Learning Brain MRI

Oct 1, 2026cs.CV

MIRTO: a registration-gated, multiverse-tested evaluation protocol for unsupervised anomaly segmentation in brain MRI

Unsupervised anomaly detection (UAD) methods for brain MRI are ranked by a single score, yet that score rests on choices that are rarely reported: how each anomaly map is aligned with the reference, how and on which data the threshold is set, and which false-positive budget, metric, aggregation and lesion definition are used. We present MIRTO, an evaluation protocol that makes these choices explicit and measures their effect. It gates the geometry of every comparison with a registration check and label-free diagnostics of known power, sets thresholds on validation data alone and reports the false-positive volume actually realised on test, repeats each comparison over 15,552 defensible evaluation pipelines, and attaches paired subject-bootstrap intervals with multiplicity control. Applied to four UAD methods trained on the same healthy data and tested on 312 BraTS 2020 subjects, MIRTO showed that an axis-order mismatch between stored maps and the reference lowered a diffusion model's voxel AUROC from 0.873 to 0.583 whilst barely moving its slice-level AUROC. Within each metric, the method explained at least 0.95 of the variance in voxel AUROC and AUPRC and 0.77 in Dice, but only 0.14 in lesion sensitivity, where the lesion definition and hit criterion dominated. A Dice advantage that was significant at validation thresholds vanished at equal realised false-positive burden, and an exact identity attributes it to threshold transfer. A training-free change to REFLECT's latent aggregation raised Dice at equal burden by 0.052. Nine hypotheses were tested against explicit criteria; because the same cohort served to develop the protocol, all inference is exploratory.

Negin Kafee Hernashki, Soumick Chatterjee

Università degli Studi di Milano, Milan, Italy · Politecnico di Milano, Milan, Italy · Human Technopole, Milan, Italy +1

Anomaly Localization Unsupervised Anomaly Detection Medical Image Benchmarks Brain MRI

Oct 1, 2026cs.CV

Surface-volume self-supervised representation learning of brain MRI for genetic discovery

Existing genome-wide association studies (GWAS) of brain imaging provide predefined or deep-learning-derived imaging phenotypes, yet these phenotypes come from either volumetric scans or cortical surface meshes, so each captures only part of the heritable variation in brain anatomy. Here we introduce MEVA (Mesh-Enhanced Volumetric Autoencoder), a self-supervised framework that encodes voxel-level image intensity together with cortical mesh geometry, including curvature and cortical thickness at each surface vertex, into one shared set of imaging features. Combining the mesh and volumetric inputs in MEVA yields modest performance gains in age and sex prediction over models that use either input alone. When these features serve as phenotypes for GWAS in the UK Biobank, they reveal more genome-wide significant loci than features learned from volumes alone or from meshes alone. These results suggest that adding cortical surface geometry to volumetric self-supervised learning captures additional heritable variation and so increases the number of loci detected.

Tian Xia, Nuo Chen, Zihao Zhu +4

D. Bradley McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, US. · Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, US. · Department of Electrical and Computer Engineering, Texas A&M University, College Station, US. +1

Self-Supervised Learning Medical Image Representation Learning Brain MRI Multimodal Learning

Sep 30, 2026cs.CV

Scores That Hold, Benchmarks That Leak: Measuring Dataset Contamination in Public Brain-Tumor MRI Classification

Automated classification of brain tumors from MRI is a heavily published application of deep learning in medical imaging, with reported accuracies on public benchmarks routinely exceeding 98%. However, accuracy does not capture a critical dimension of benchmark quality: dataset integrity, defined as the independence of test from training data at the image, patient, and acquisition-source levels. We introduce a three-layer contamination framework comprising duplicate, patient, and source-label leakage to assess the public corpora on which this literature rests. We audit the three most widely used corpora against a chest-radiograph negative control and quantify each layer's effect on measured performance across nine architectures and three evaluation conditions. Contamination is severe at every layer: 28.8% of the dominant corpus's official test split has a near-twin in its own training split, a second corpus leaks 22.3% of its test images byte-identically, 95.5% of traceable test images share a patient with training, and file-header features containing no anatomy separate tumor from no-tumor at 0.959 balanced accuracy, at parity with fine-tuned ResNet backbones. The unexpected result is that removing every identified leaked test image leaves balanced accuracy essentially unchanged: stable performance after deduplication does not establish benchmark integrity. Our findings establish dataset integrity as a distinct, measurable axis of benchmark quality that a stable leaderboard cannot certify. For biomedical research, reported accuracy on these corpora alone does not establish that a model has learned to recognize tumors rather than exploit dataset-specific cues. We release the contaminated-file lists, recovered patient identifiers, and deduplicated splits.

Bhanu Prakash Vangala, Sowmya Guda, Latha Peddi +1

Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA · Government Degree College (Autonomous), Siddipet, Telangana 502103, India · Amar Biotech Private Limited, Kondapur, Hyderabad, Telangana 500084, India

Data Leakage Benchmark Contamination Brain Tumor Classification Medical Image Benchmarks Brain MRI

Sep 30, 2026cs.CV

MRI Super-Resolution with RCDM/WaveMix and Task-Aware Segmentation

Super-resolution and quality enhancement of 1.5,T brain MRI are normally validated with image-fidelity metrics, although their purpose is to improve downstream analysis. We study whether enhancement improves tissue segmentation, and for which segmenters. We propose an unpaired, physics-guided training pipeline for a lightweight (

\le

2.5,M parameter) recurrent convolutional enhancer: a six-module stochastic 1.5,T degradation operator, a residual adversarial network that adds scanner-specific texture without moving anatomy, and a cycle-consistent objective with an anti-identity penalty that rules out the copy solution. We then train U-Net, Swin-UNet and wavelet token-mixing segmenters \citep{jeevan2023wavemix} from scratch on either raw or enhanced 1.5,T images of the same subjects, using identical labels and subject-level splits, for three enhancer variants and two datasets. On ABIDE (41 held-out subjects, FreeSurfer labels) enhancement significantly improves the wavelet segmenter (mean Dice

+0.014

, Wilcoxon

p=3.5\times10^{-5}

; CSF

+0.018

, grey matter

+0.013

), significantly degrades the U-Net (

-0.008

,

p=5.1\times10^{-4}

) and leaves Swin-UNet unchanged. On IXI, whose labels come from FSL-FAST, enhancement lowers Dice for all nine pairings, almost entirely through CSF; we trace this to spatially implausible CSF voxels in the labels that penalise smoother predictions. Enhancement of low-field MRI should therefore be validated per downstream model and against reliable labels.

Kavitha Viswanathan, Harsh Choudhary, Amit Sethi

Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai 400 076, India

Medical Image Analysis Medical Image Super-Resolution Medical Image Segmentation Unpaired Image-to-Image Translation Brain MRI

Sep 28, 2026cs.CV

Reduce, Then Encode: Multiscale Volumetric Reduction for 2D Foundation Models in Brain MRI

Pretrained 2D foundation models offer a practical alternative to dedicated 3D pretraining for brain structural magnetic resonance imaging (sMRI), but their use on volumetric data requires bridging the mismatch between a 2D encoder and a 3D volume input. Existing methods typically encode slices independently and integrate their features afterwards. We introduce Multiscale Volumetric Reduction (MVR), a reduce-then-encode approach that compresses each anatomical view from (D) slices into (M << D) complementary 2D components before foundation-model encoding. MVR combines an uncentered-PCA base component derived from the original through-plane intensities with residual detail components constructed from multiscale spatial descriptors. The reduction is estimated from the training volumes without diagnostic labels or gradient-based optimization and remains fixed thereafter. The resulting components are independently processed by a shared frozen 2D foundation model and concatenated for linear probing. Under this frozen-encoder setting, MVR achieves strong overall performance across ADNI, OASIS, and ABIDE relative to the evaluated 2D-to-3D adaptation methods and simple input-reduction baselines, while also generalizing strongly from ADNI to AIBL.

Dexuan Ding, Yuankai Qi, Bogong Wang +2

Macquarie University · Australian National University · University of Sydney

Medical Imaging Foundation Models Dimensionality Reduction Brain MRI

Sep 28, 2026cs.CV

Evidence Before Accuracy: A MRI-PET Fusion Network for Alzheimer Disease Classification with Causal Regional Validation

Deep learning models for Alzheimer disease (AD) classification routinely report near-perfect discrimination, yet few are shown to rest on AD-relevant neurobiology rather than on dataset artifacts, subject-level leakage, or non-brain image content. We present a fusion network combining T1 MRI and FDG PET across axial, coronal, and sagittal planes, trained on ADNI consists of 554 paired subjects. The fusion model reaches AUC 0.962, accuracy 0.909, and F1 0.891, competitive with recent 3D CNN and multimodal transformer systems at substantially lower cost. We first quantify how much modality, plane and slice geometry matter. A validation-only search over slice centres and neighbour spacings moves AUC by 0.180 for MRI and 0.078 for PET, selecting narrow spacing for MRI and wide spacing for PET, with the chosen coronal centres falling on the hippocampal body and on the posterior cingulate respectively. The contribution, however, is the evidence layer built around that number. Shortcut controls collapse the model to AUC 0.622 (silhouette), 0.608 (exterior), and 0.500 (blank), and a label-permutation null yields 0.456. Forward region-of-interest (ROI) ablation shows that masking medial temporal cortex in MRI and the posterior default-mode network (DMN) in PET produces the largest shift in the AD logit, while area-matched controls remain indistinguishable from that null. Reverse ROI ablation shows that the medial temporal lobe alone retains 89.2% of above-chance discrimination in MRI and the posterior DMN alone retains 79.0% in PET. A quantitative comparison of attribution methods shows occlusion sensitivity reaching 3.5-5.0* enrichment inside a priori AD regions against 0.10-0.43* in controls. Ablation and attribution independently establish a biologically correct double dissociation: hippocampal evidence is carried by MRI, posterior cingulate evidence by PET.

Saeid Firouzi Daghigh, Saeed Ayat

Department of Computer Engineering and Information Technology, Payame Noor University, Tehran, Iran

Alzheimer's Disease Classification Explainable Medical Image Analysis Multimodal Fusion Brain MRI

Sep 21, 2026cs.CV

WebMRIQC: A Web-Based Implementation of MRIQC for Accessible MRI Image Quality Assessment in Resource-Constrained Settings

Reliable quality control (QC) of magnetic resonance imaging (MRI) is essential for reliable diagnostic neuroimaging, yet standard manual assessment is subjective and time-consuming. MRIQC has established standardized automated extraction of image-quality metrics (IQMs), but its reliance on local computational imaging skills and capacity including high-performance computing, limits its adoption in resource-constrained settings (RCS). We present WebMRIQC (webmriqc.mailab.io), an open-source browser-based platform that wraps the validated MRIQC engine behind a zero-installation web interface. WebMRIQC automates the DICOM-to-BIDS conversion of de-identified MRI scans, executes the unmodified containerized MRIQC pipeline on a shared compute node governed by a fair-share job queue, and returns an interactive in-browser dashboard. The dashboard grounds every IQM in published quality thresholds, benchmarks each scan against the normative distribution of high-resource open datasets, and supports cross-site multicentre implementation of optimized scan protocols in RCS.We describe the system architecture and a validation framework establishing measurement equivalence between WebMRIQC and native MRIQC across thirteen IQMs on the BraTS-Africa and BraTS 2021 datasets. Preliminary results indicate strong agreement for contrast-, signal and noise-based metrics, demonstrating that web-based implementation lowers the barrier to standardized MRI QC and provides a foundation for harmonized, regionally adapted quality benchmarks across RCS imaging sites. The code is publicly available here https://github.com/CAMERA-MRI/WebMRIqc.

Philip Nkwam, Ifeoluwa Oladeji, Sekinat Zurakat-Aderibigbe +9

Department of Radiography, Faculty of Health Professions, College of Medicine, University of Lagos, Nigeria. · Medical Artificial Intelligence Laboratory, Crestview Radiology Ltd., Lagos, Nigeria. · Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada. +3

Medical Image Analysis Magnetic Resonance Imaging Image Quality Assessment Brain MRI

Sep 21, 2026cs.CV

Evaluating the Generalization of Neuroimaging Foundation Models on African Brain MRI

Neuroimaging foundation models pretrained on large, predominantly western cohorts are increasingly proposed as general-purpose backbones for brain MRI analysis. Yet, their ability to generalize to underrepresented clinical populations remains largely untested. We evaluate four recent foundation models (BrainIAC, Neuro-JEPA, NeuroVFM, and Primus) on a three-way diagnostic classification task (Control, Dementia, Parkinson's disease) using a cohort of 88 subjects from a Nigerian clinical brain MRI dataset, across four modality configurations (T1w, T2w, T1w+T2w, FLAIR), and compare against an end-to-end trained ViT3D baseline. The frozen backbones collapse to majority-class predictions, while Neuro-JEPA on FLAIR shows modest but still limited discrimination. In contrast, the end-to-end trained ViT3D achieves higher accuracy and MCC on every task (up to 53.4% accuracy, MCC=0.27) and is the only model with non-trivial recall. Our findings suggest that these frozen neuroimaging foundation models are insufficient for fine-grained diagnostic classification in small, non-western clinical cohorts, motivating parameter-efficient adaptation and broader multi-site external validation for equitable deployment in global health settings.

Oluwatobi Iyanuoluwa Akinmuleya, Olatokun Shamsudeen Akano, Samuel Danquah Ankapong +2

Department of Medicine, Shenyang Medical College, Shenyang, China · College of Medicine, University of Ibadan, Ibadan, Nigeria · University of Ghana, Accra, Ghana +2

Medical Imaging Foundation Models Domain Generalization Medical Image Classification Brain MRI

Sep 17, 2026cs.CV

Fast Cross-Strength Multi-Contrast Brain MRI Translation using Latent Bridge Matching

Magnetic Resonance Imaging (MRI) acquired at different field strengths exhibits pronounced variation in noise, resolution, homogeneity, and contrast, which limits comparability across acquisition settings and complicates downstream analysis. We address this with a unified conditional model for controllable field-to-field synthesis, built on the framework of conditional latent bridge matching. Our single model achieves highly competitive results across the validation phase for all three tasks of the MRIxFields2026 challenge without task-specific architectures or training. We achieve fast generation with only a single inference step, producing all modality and field-strength combinations for

30

axial slices in under

90

seconds, as well as cross-modality-strength translation for a full volume in under

70

seconds, on a single NVIDIA A5000 GPU. We further provide extensive ablations regarding different components of our solution. Code: https://gitlab.com/siddharthsrivastava/mrixfields-2026

Siddharth Srivastava, Till Bretschneider

University of Warwick, United Kingdom

Magnetic Resonance Imaging Medical Image Synthesis Brain MRI

Sep 11, 2026cs.CV

Brain-PACE: A Deep Siamese MRI Framework for Modelling Longitudinal Brain Acceleration

Brain age estimation has become a popular research proxy for assessing brain health and disease, yet longitudinal trajectories of brain ageing are still poorly defined, and clinical use is limited. Building on existing Siamese longitudinal frameworks, we develop Brain-Predicted Age Acceleration (Brain-PACE) to directly estimate the pace of structural brain ageing from paired T1-weighted MRI. Brain-PACE identified accelerated ageing in

42.6

% of participants with mild cognitive impairment. Faster Brain-PACE was associated with greater functional and cognitive impairment (FAQ;

r=0.35

, ADAS13;

r=0.30

, CDR-SB;

r=0.32

) and greater regional tau burden in the posterior cingulate (

r=0.59

), precuneus (

r=0.47

), and entorhinal cortex (

r=0.37

). These associations were stronger than those observed when pace was calculated indirectly from repeated cross-sectional brain age estimates, suggesting that direct longitudinal modelling captures complementary information relevant to ongoing pathological change. Methodologically, Brain-PACE extends the LILAC framework by combining spatial attention with soft label distribution learning and a Cram'er distance objective, improving probabilistic performance and reducing prediction bias while providing measures of predictive uncertainty. Together, these findings support Brain-PACE as a complementary longitudinal imaging phenotype with sensitivity to relevant clinical and biological changes in early neurodegeneration.

Samuel Maddox (School of Computing Sciences, University of East Anglia), Jacob Newman (School of Computing Sciences +8

School of Computing Sciences, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK · Norwich Medical School, University of East Anglia Norwich Research Park, Norwich, NR4 7TJ, UK

Alzheimer's Disease Brain Age Prediction Longitudinal Medical Image Analysis Siamese Neural Networks Brain MRI

Sep 9, 2026eess.IV

Scale-Aware 3D Deep Learning for Robust Brain Metastasis Detection in Multimodal MRI

Detecting brain metastases in magnetic resonance imaging (MRI) remains challenging because lesions vary widely in size and appearance, with very small metastases occupying only a minute fraction of a three-dimensional input. We investigate whether combining different spatial fields of view (FOVs) improves lesion detection in multimodal MRI and present a scale-aware 3D deep-learning framework. The method uses independently trained

96^3

and

64^3

3D U-Nets whose whole-volume probability maps are combined by weighted late fusion. This design allows us to study the effect of spatial context separately from image resolution and modality choice. On a 97-patient development cohort, cross-FOV fusion improved lesion-level precision and F1 while substantially reducing false positives relative to the individual models. A same-FOV ensemble control showed that these gains were not explained solely by averaging independently trained networks, supporting a contribution from complementary spatial context. An exploratory cross-FOV agreement filter reduced false positives but did not improve overall F1. These results support cross-FOV probability fusion as a simple and computationally practical strategy for improving the precision-false-positive trade-off in 3D brain-metastasis detection.

Sylvain Jaume, Hongming Wang, Simon K. Warfield

Massachusetts Institute of Technology · Harvard University · Boston Children’s Hospital, Harvard Medical School

3D Medical Imaging 3D Medical Image Segmentation Brain MRI

Sep 7, 2026eess.IV

Spatial Feature-wise Linear Modulation (SpFiLM) for Contrast Agent-Aware Brain Parcellation

Most automated brain parcellation tools are developed and validated on T1-weighted (T1w) MRI. Yet, some clinical workflows for which parcellation is relevant only use contrast-enhanced T1w (T1ce) MRI, on which T1w-trained models are less accurate. We present a unified network that parcellates both pre- and post-contrast agent T1w MRI reliably, trained on a combination of the two with conditioning that spatially modulates its response differently for each. Feature-wise Linear Modulation (FiLM) is a known approach for input-based modulation in networks. It applies a per-channel scale and shift uniformly across the input. However, the appearance change between pre- and post-contrast varies locally across the brain, making FiLM suboptimal for our use case. In this work, we introduce Spatial FiLM (SpFiLM), a conditioning layer whose modulation varies spatially, assembling a voxel-wise scale and shift from image-derived spatial patterns. Using a cohort of 134 patients with paired T1w and T1ce MRI parcellated into 106 classes, the addition of SpFiLM layers in a UNet increased the mean Dice on the test set of 25 patients from 80.2% to 84.1%, a 4.9% relative improvement. Adding SpFiLM layers led to the best performance on both pre- and post-contrast MRI, even when controlling for network parameter counts.

Pushpendra Singh, Joshua R. Astley, Roman Rodionov +3

School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK · School of Biomedical Engineering and Imaging Sciences, King’s College London, London, UK · Department of Epilepsy, Queen Square Institute of Neurology, University College London, London, UK

Medical Image Segmentation Neuroimaging Brain MRI

Sep 2, 2026eess.IV

LoFi RADIO: A Distilled In-Domain Backbone Applied for Artifact-Severity Grading of Ultra-Low-Field Neonatal Brain MR

Ultra-low-field MRI makes neonatal brain imaging deploy- able in low-resource settings, but its low SNR, lack of shielding, and long scan duration make it especially prone to acquisition artifacts, motivating automated quality control. We address the LISA 2026 Task 1a challenge: multi-label severity grading (0/1/2) of seven common image artifacts on ULF T2 weighted volumes. We identify that a number of backbones may be successfully paired with a classification MLP, but that no single backbone is uniformly best across artifacts. To improve performance, we evaluate routing complementary foundation model teachers through a per-artifact gate, as well as distilling the teachers into a single in-domain ViT-S student (LoFi RADIO) over an unlabeled low-field MRI corpus. Both of these strategies improve the weighted composite. The distilled backbone matches or exceeds the gate and has the added advantage of not requiring deployment of multiple large foundation models at infer- ence.

Jonathan B. Martin, Yashwant Kurmi, Charlotte R. Sappo

Vanderbilt University Institute of Imaging Science, Nashville, TN, USA

Medical Image Analysis Magnetic Resonance Imaging Brain MRI Vision Transformer Knowledge Distillation

Sep 2, 2026cs.CV

The Diagnosis a Reporter Leaves Unspoken: Surfacing Frozen Tumor Features for Brain-Tumor MRI Reporting

A capable brain-MRI report generator can still be, in effect, diagnostically silent. When a multi-chain chain-of-thought (CoT) reporter built on a medical Mistral-7B backbone is evaluated on held-out cohorts, it names most meningiomas and almost all metastases "glioma" (diagnosis recall 0.44/0.07). Yet the answer is not absent from the model: a supervised linear probe applied to its frozen segmentation features recovers the three tumour cohorts at 0.82 macro-F

_1

(5-fold cross-validation; chance

\approx

0.33). We introduce NeuroFusion, an assistive reporter that surfaces this latent signal rather than overriding it: discriminative field-classifier heads over per-lesion features condition a fast, single-pass draft-then-review decoder on their committed outputs. Built on the identical Mistral backbone, this restores the diagnosis (meningioma 0.92, metastasis 0.75) and wins 8 of 9 prose-content comparisons across three held-out cohorts (RaTEScore, RadGraph-F

_1

, GREEN; Holm-corrected paired BCa), with no significant loss on the ninth, at 5-6x lower latency (

\approx

80 vs. 457 s/case). A controlled negative result sharpens the mechanism: a learned diagnosis pin that overrides the decoder instead of merely informing it collapses out-of-distribution metastasis recall to 0.03. Grammar-constrained decoding keeps 92.3% of records schema-valid, making every sentence entailment-checkable (7.5% contradicted vs. 36.8% for the direct baseline). In a blinded nine-case pilot, two board-certified neurologists independently rated NeuroFusion highest in every tumour type, the only system with zero critical errors, and gave it the top-rated sign-off in eight of nine cases (six outright, two ties).

Khawaja Murad ul Hassan, Ruqiyya Adil, Adil Qayyum +4

National University of Sciences and Technology, Islamabad, Pakistan · Consultant Radiologist, Rawalpindi, Pakistan · Bahria University Health Sciences Campus, Islamabad, Pakistan +1

Radiology Report Generation Brain MRI Brain Tumor Classification

Sep 2, 2026cs.CV

ORB-SVM : An Innovative Hybrid Framework for Efficient Brain Tumor Detection from MRI Scans

Brain cancer remains one of the most significant challenges in modern medicine, where the accuracy of early stage diagnosis is a decisive factor in patient survival and treatment efficacy. Although Magnetic Resonance Imaging (MRI) is the established gold standard for visualizing neurological structures, the interpretation of these high dimensional scans is often complicated by subjective variability among practitioners and the inherent noise present in complex medical images. While contemporary approaches frequently rely on high parameter deep learning architectures, such models often involve significant computational costs and require extensive data for effective training. This study introduces a hybrid framework that utilizes the Oriented FAST and Rotated BRIEF (ORB) algorithm for precise feature extraction and a Support Vector Machine (SVM) for classification [1], [2]. The proposed approach achieves a sub- stantial data reduction of approximately 99.5%, which effectively minimizes the influence of non informative background data while preserving critical diagnostic patterns essential for tumor identification. By balancing feature sparsity with a robust kernel based classifier, this methodology addresses the limitations of over parameterized systems while maintaining high diagnostic integrity. Experimental evaluations conducted on the Br35H dataset demonstrate that the framework attains a classification accuracy of 97.5%. The findings suggest that the integration of localized feature representation and optimized classification provides a reliable and resource efficient alternative for medical image analysis, offering a structured solution that maintains per- formance without the need for extensive computational overhead.

Amirhosein Azarpour

Department of Computer Science Shahid Beheshti University Tehran, Iran

Medical Image Analysis Brain MRI

Sep 1, 2026cs.CV

SliceBridge: context-consistent repair of corrupted slice intervals in T1-weighted MRI

Structural magnetic resonance imaging (MRI) images are sometimes corrupted over a contiguous set of slices, where acquisition, motion, hardware, or reconstruction effects leave a single slice or short interval inconsistent with its neighbors while the rest of the image remains usable. Such localized corruption can bias downstream morphometric analysis, yet discarding or reacquiring an otherwise usable image is costly. We formulate this as an image restoration problem: given the location of the affected interval, reconstruct those slices from the surrounding anatomical and imaging context. We propose SliceBridge, a framework for restoring corrupted slice intervals in T1-weighted MRI using rectified flow matching conditioned on the surrounding intact slices and their relative slice positions. Through-plane consistency is encouraged by coupling the slices within the interval through interval-correlated initial noise, a shared flow time, and synchronized sampling. The restored interval is then inserted back, leaving all other slices unchanged. We trained and validated the model on 9,877 T1-weighted brain MRI volumes from four datasets and evaluated it on 581 external subjects using clean interval withholding and controlled corruptions. Compared with a matched model that reconstructed target slices independently, SliceBridge reduced error in slice-to-slice changes within repaired intervals by 32.9%-41.3% across interval lengths and achieved higher SSIM at every interval length. In controlled-corruption cases, SliceBridge reduced the median error in regional brain volume estimates produced by a downstream segmentation model from 1.95% in corrupted volumes to 1.05%.

Jiheng Li, Michael E. Kim, Trent Schwartz +6

Department of Computer Science, Vanderbilt University, Nashville, TN, USA · Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA · Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA

Magnetic Resonance Imaging Image Restoration Image Inpainting Brain MRI

Sep 1, 2026cs.CV

Conditional Flow Matching for Cross-Field MRI Harmonisation

Magnetic resonance images of the same subject look markedly different across field strengths, which complicates the comparison and pooling of data across sites. We address cross-field brain-MRI translation for the MRIxFields2026 challenge, and in particular its Task~3: a single model that translates between any directed pair of the five field strengths and across three contrasts. We phrase the problem as a conditional flow matching path: because the source and target volumes are spatially registered, we learn a velocity field that carries the source slice directly to the target slice, rather than starting from noise. To learn this mapping from only three paired subjects, the unified model is trained in three stages: a degradation-bridge pretraining that distills a restoration prior from the abundant unpaired retrospective cohort, a cross-field finetuning over all directed pairs on the paired cohort, and an adversarial refinement that sharpens the output. At inference, we integrate the learned velocity with a second-order Heun solver in a handful of steps. A restoration prior learned without any paired data already reaches a mean SSIM of 0.837, and each subsequent training stage improves on it. A single 6.3M-parameter model thereby covers all 60 field-pair and contrast combinations, with inference in five solver steps per slice. On the challenge evaluation set the model reaches a mean SSIM of 0.909, averaged over the three contrasts, outperforming regression and diffusion baselines built on the identical network on all three challenge metrics.

Baris Imre, Aram Salehi, Levente Baljer +3

Division of Image Processing, Department of Radiology, Leiden University Medical Center · Department of Human Genetics, Radboud University Medical Center · Department of Radiology, Leiden University Medical Center +2

Conditional Flow Matching Magnetic Resonance Imaging Medical Image Synthesis Brain MRI

Sep 1, 2026cs.CV

BrainDiff: Longitudinal Report Generation for Multimodal Brain MRI

Neuroradiologists rarely read a brain MRI in isolation, yet automated brain-MRI report generation has been built almost entirely for single studies. Temporal analysis has been explored on chest radiography and chest CT, but to our knowledge, longitudinal reporting for brain MRI, where interval change is often subtle and spatially distributed, remains unaddressed. We present BrainDiff, the first longitudinal vision-language system for brain MRI. BrainDiff outperforms both frontier general-purpose and single-study neuroimaging models on the same patient pairs. Moreover, BrainDiff retains 91% of internal RadGraph-XL entity+relation F1 (rg_er) on an external, cross-hospital cohort. Beyond the system, we contribute three analyses. First, we identify two independent grounding levers: a counterfactual objective with prior-report dropout, which increases measured image reliance by ~47%, and a staged curriculum. Together, these interventions raise image reliance 2.5-fold from the baseline. Second, we provide a factorial over prior-report availability and image identity, isolating a visual contribution of +0.0387 rg_er, which grows when the prior report is withheld. Third, a cheap change-decodability test for candidate backbones shows that interval change is decodable far more weakly than single-study pathology (0.60 vs. 0.77 AUROC). Code is publicly available at https://github.com/jhuldr/BrainDiff.

Krish Patel, Peirong Liu

Department of Electrical and Computer Engineering, Data Science and AI Institute, Johns Hopkins University

Radiology Report Generation Longitudinal Medical Image Analysis Medical VLMs Brain MRI

Aug 27, 2026cs.CV

Tissue-Mixture Entropy-Weighted Reconstruction for Partial-Volume-Aware Brain MRI Super-Resolution

Background and Objectives: Full-image objectives in brain magnetic resonance imaging (MRI) super-resolution (SR) can underweight tissue-transition regions affected by the partial-volume effect (PVE), as these regions occupy a small fraction of the image. Binary boundaries further provide only a discrete approximation of continuous tissue mixtures within a voxel. Methods: We propose Anatomy-Guided Gaussian-Parameter Warping with PVE-Balanced Reconstruction (AGW-PBR), combining a low-resolution (LR)-only reconstruction backbone with a PVE-aware training objective. The backbone uses LR-derived anatomical guidance, soft latent assignment, and bounded residual warping. Quality-controlled tissue fractions are converted into tissue-mixture entropy to spatially weight reconstruction within validated PVE support. PVE sidecars are used only during training, while inference requires only the LR image. Downstream utility is further evaluated through zero-shot transfer to whole-tumor segmentation on BraTS2023. Results: AGW-PBR improves reconstruction across 2x and 4x SR on IXI and achieves the lowest normalized gradient-vector reconstruction error at both CSF--GM and GM--WM interfaces at 4x. Ablation studies verify the contributions of PVE-aware weighting and soft latent assignment. The PVE-free AGW backbone also maintains strong performance on fastMRI. On BraTS2023, AGW-PBR achieves competitive whole-tumor Dice and the lowest HD95 under direct zero-shot transfer. Conclusions:AGW-PBR improves brain MRI SR while preserving tissue-transition information relevant to downstream analysis. The results support tissue-mixture entropy as an effective supervision signal for partial-volume-aware MRI reconstruction.

Xiao Tong, Wenyun Yang, Ziheng Zhang +3

aState Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, P. R. China · bWeihai Institute of Oceanology, Peking University, Weihai, 264209, P. R. China · cBeijing MagnVue Medix Co., Ltd., Beijing, 100085, P. R. China

Medical Image Super-Resolution Brain MRI Adaptive Loss Weighting

Aug 24, 2026cs.CV

AnaDiffusion: Anatomically CompositionalLatent Diffusion for Controllable 3D Brain MRI Generation

3D brain MRI generation has made significant advances in medical imaging, simulation, and controllable anatomical analysis. However, existing generative models typically synthesize 3D volumes monolithically, often overlooking regional anatomical structures and limiting local controllability. To address these limitations, we introduce AnaDiffusion, an anatomically compositional latent diffusion framework that factorizes the generation process into distinct, anatomically meaningful regions, followed by part-to-whole assembly and global refinement. Our approach first trains part diffusion models to capture local structural priors. We then inject an assembled anatomical composite of the parts into the whole-brain latent representation and continue denoising. This mechanism enables the model to resolve global context while preserving the injected anatomy. As a result, AnaDiffusion produces both explicit part assets and a globally coherent volume, thereby enabling controllable part editing without requiring subject-specific dense segmentation maps at inference time while maintaining consistent part-to-whole brain structure. On the subject-disjoint ADNI test split, AnaDiffusion achieves the lowest FID across the whole brain, left and right hemispheres, cerebellar-brainstem complex, and seam regions. It also achieves the best cerebellar and second-best ventricular and brainstem absolute Cohen's d values among the evaluated methods. In localized editing experiments, paired MS-SSIM demonstrates high target transfer and off-target preservation, supporting controllable part replacement with minimal unintended anatomical alterations.

Huiwen Han, Lulin Liu, Bangya Liu +8

Stanford University · Texas A&M University · University of Minnesota +4

Compositional Image Generation Medical Image Synthesis Controllable Image Generation 3D Diffusion Models Brain MRI

Aug 10, 2026cs.CV

Frozen Brain-MRI Foundation Models Are Site Fingerprints

Frozen foundation-model (FM) embeddings are increasingly used as off-the-shelf brain-MRI representations, on the assumption that they capture anatomy. We audit what they actually encode and find that acquisition site is a large, intrinsic component of the representation. Across two independent cohorts (ABIDE-I, ABIDE-II), three frozen 3-D encoders (brain-pretrained, CT-pretrained, and randomly initialized), and every network depth, site is linearly decodable at roughly 0.9 balanced accuracy at deep layers, exceeding the decodability of every clinical or demographic variable (sex, age, autism diagnosis) at every layer. The effect is intrinsic rather than learned: a randomly initialized encoder is already a ~0.9 site classifier on both cohorts and across three architecture families (Swin, ViT, ResNet), and site is decodable at ~0.95 directly from the raw downsampled image with no encoder, so the fingerprint reflects low-level image statistics that any encoder preserves rather than a product of pretraining. Residualizing measured population covariates leaves site decodability essentially unchanged, indicating an acquisition- rather than population-driven effect. A nonlinear probe matches the linear one, so the fingerprint is fully linearly accessible. The site subspace is removable post hoc by iterative null-space projection or ComBat (site decodability 0.94 -> 0.07/0.00), and is a site-attribution concern for shared or federated embeddings; but for dense segmentation this removal is not free, because site and anatomy occupy an entangled linear subspace (a matched-rank random-direction projection is Dice-neutral, whereas removing the site subspace is destructive). We recommend site-audited use of frozen brain-MRI FMs and release an open audit toolkit.

Saman Rahbar

University of British Columbia, Vancouver, Canada

Medical Imaging Medical Imaging Foundation Models Medical Image Analysis Medical Image Representation Learning Brain MRI

Aug 10, 2026cs.CV

Motion Artifact-Aware Self-Supervised Representation Learning for 3D Brain MRI Motion Artifact Reduction

Patient motion remains a source of image degradation in brain MRI, leading to signal loss, blurring, and geometric distortion that compromise quantitative analysis. Existing deep learning methods for motion correction typically rely on paired clean-corrupted data or k-space acquisitions, which are rarely available in clinical settings. We propose SSRL-MAR, a motion artifact-aware unpaired representation learning framework for motion artifact reduction that requires neither paired training data nor explicit motion labels. SSRL-MAR employed a three-stage training strategy: (1) contrastive learning on 3D patches to extract motion representations by contrasting clean and synthetically corrupted images, (2) a motion artifact-aware synthesis network to generate motion artifacts from clean scans, and (3) a motion artifact-aware generator to restore clean volumes using the learned degrader for self-supervised supervision. On in-silico dataset, SSRL-MAR achieved PSNR 23.81dB, SSIM 91.55%, and NMSE 0.79%. On in-vivo MR-ART dataset, the pretrained model reduced motion distortion, and unsupervised domain adaptation further improved anatomical fidelity. Against a source-only supervised model trained on the same simulated pairs, SSRL-MAR improved PSNR by up to 2.0 dB on MR-ART after unsupervised domain adaptation, and remained within 0.25-0.47 dB of an oracle supervised model that requires real paired data unavailable in practice. At the milder motion level, volumetric error in structures such as the corpus callosum and ventricular system decreased by more than 50%, confirming improved neuroanatomical consistency. These results indicate that SSRL-MAR provides a robust and scalable image-domain solution for 3D brain MRI motion correction, enabling reliable structural quantification in large-scale neuroimaging studies without requiring prospectively acquired pairs or acquisition-specific calibration.

Mojtaba Safari, Shansong Wang, Zach Eidex +4

Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, USA · Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, USA · Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA +1

Magnetic Resonance Imaging Medical Image Representation Learning Brain MRI

Aug 9, 2026cs.CV

MRI super-resolution in ten sampling steps using a diffusion bridge model

Objective. MRI provides excellent soft-tissue contrast, but long acquisition times can cause patient discomfort and lead to motion artifacts, forcing a trade-off between spatial resolution and scan time. Diffusion-based super-resolution (SR) reconstructs high-resolution (HR) images from low-resolution (LR) inputs, but typically needs many sampling steps and initializes from a Gaussian prior ill-suited to image restoration. We developed an efficient diffusion framework that reconstructs HR MRI directly from LR data. Approach. We propose super-resolution diffusion bridge model (SR-DBM), a super-resolution diffusion bridge model that casts SR as a stochastic transport between the LR and HR image distributions. Through a Doob's h-transform of a mean-reverting stochastic differential equation, SR-DBM pins the process to the paired HR and LR images at its endpoints, initializing reconstruction from the measured anatomy rather than from Gaussian noise. The HR image is recovered by a deterministic reverse trajectory in which a network predicts the clean image at each of only ten sampling steps. We evaluated SR-DBM on ultra-high-field 7T brain T1 MP2RAGE maps and pelvic T2-weighted prostate images against nine comparison methods using PSNR, SSIM, GMSD, and LPIPS. Main results. SR-DBM attained the highest PSNR and SSIM and the lowest GMSD on both datasets (brain: 27.66+-1.52 dB, 0.96+-0.02, 7.96+-1.86$; prostate: 27.87+-2.29 dB, 0.80+-0.05, 8.38+- 1.44), with statistically significant gains over every comparison method (two-sided Wilcoxon signed-rank test with Holm correction, p<0.05). The strongest baseline, SR-EMamba, ranked second. Qualitatively, SR-DBM produced the smallest residual errors and best preserved fine structures and lesions.

Mojtaba Safari, Hang Yu, Zach Eidex +10

Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL, United States · Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States · Department of Radiation Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, United States +3

Medical Image Super-Resolution Diffusion-Based Inverse Problems Diffusion MRI Diffusion Model Acceleration Brain MRI Diffusion Models

Aug 9, 2026cs.CV

Anatomically Consistent Cross-Contrast Super-Resolution of Anisotropic Brain T2w MRI

T2-weighted (T2w) brain MRI provides fluid-sensitive soft-tissue contrast that is important for neuro-oncology and radiotherapy planning. However, T2w scans are acquired with anisotropic voxels and appear blurred or stair-stepped on coronal and sagittal views, which obscures small structures and weakens any downstream 3D analysis. We propose VIPP-SR (View-Independent Patched Projection Super-Resolution), a cross-contrast guided super-resolution framework that restores the inter-plane resolution of an existing anisotropic T2w volume without an isotropic ground-truth T2w. VIPP-SR first trains a view-independent patched generator (VIP-GAN) to learn local T1c-to-T2w anatomical correspondence from high-resolution axial slices. The trained generator is then applied to axial, coronal, and sagittal views of the T1c volume to generate three orthogonal T2w estimates. Shape-preserving patching and deepest-skip removal reduce view-specific shortcuts, thereby constraining the generator to learn patch-local representations and enabling the zero-shot inter-plane transfer. Central to VIPP-SR, a projection-based optimization then enforces anatomical consistency across the three view-specific volumes, fusing them by balancing inter-plane self-consistency against per-view data fidelity. The generator is trained on BraTS-MET and evaluated on both the held-out BraTS-MET testing set and the BraTS-GLI cohort without retraining, assessing the cross-cohort generalizability. The results validate that VIPP-SR improves downstream segmentation over the real anisotropic T2w baseline, raising mean-label Dice from 0.330 to 0.465 on BraTS-MET and, zero-shot, from 0.473 to 0.563 on BraTS-GLI and ablation studies identify inter-plane self-consistency as the main source of the gain.

Mengqi Shen, Haicheng Wang, Meghna Trivedi +4

Data Science Institute, Columbia University, New York, NY, USA · Department of Mechanical and Materials Engineering, University of Cincinnati, Cincinnati, OH, USA · Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA +2

Medical Image Super-Resolution Brain MRI Generative Adversarial Networks

Aug 8, 2026cs.CV

A continually expandable foundation model for brain MRI

Brain magnetic resonance imaging (MRI) is central to neuroscience and clinical assessment, but models are commonly developed for individual diseases, populations or imaging protocols. Foundation models promise more general representations, yet they are usually pretrained once and can lose earlier capabilities when updated with new data. Here we show that Alcmaeon, a three-dimensional brain MRI foundation model pretrained without manual labels on more than 425,000 volumes and derived imaging maps, can be expanded sequentially across clinical domains. Alcmaeon combines volumetric encoding and latent diffusion generation with Graph-Blueprint Pruning (GBP), which protects network modules important to earlier domains while leaving the remaining capacity trainable. Across expansion from healthy ageing and neurodegeneration to developmental, psychiatric and tumour imaging, GBP showed less forgetting than sequential adaptation and elastic weight consolidation across voxel-level reconstruction measures, with its largest advantage after adaptation to tumour imaging. The blueprints provided an inspectable record of how model capacity was protected and reused. Representations from different model levels supported image synthesis, disease classification, survival modelling and postoperative prediction, although no single representation was optimal for every task. These findings provide a route towards brain MRI foundation models that can grow with emerging data while retaining earlier capabilities.

Michail Mamalakis, Carmen Jimenez-Mesa, Yonghao Li +8

1*Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, Cambridgeshire, United Kingdom. · Department of Computer Science and Technology, University of Cambridge, 15 JJ Thomson Ave, Cambridge, CB3 0FD, Cambridgeshire, United Kingdom. · Department of Psychiatry, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, Cambridgeshire, United Kingdom. +7

Medical Imaging Foundation Models Continual Learning Brain MRI Catastrophic Forgetting Neural Network Pruning

Aug 8, 2026eess.IV

$\texttt{DisMorph}$ : learning to disentangle technical distortions from true biological change

Longitudinal MRI enables sensitive measurement of structural brain change for studying aging and neurodegenerative disease. Deformable image registration is a key tool for estimating such change by computing a dense deformation that captures geometric differences between longitudinal scans. However, MRI scanners introduce geometric distortions that vary across acquisition systems and protocols, such as gradient non-linearity (GNL) distortion. Existing registration methods estimate a single field that conflates biological and technical effects, potentially biasing downstream morphometric measurements if distortions remain (partially) uncorrected. We propose

\texttt{DisMorph}

, a registration framework trained entirely on synthetic data that explicitly decomposes longitudinal deformation into technical and anatomical transforms. It predicts two dense deformations, each encoding one effect. During training, a novel generative model synthesizes both effects separately to provide disentanglement supervision, while domain randomization promotes generalization across imaging protocols. We evaluate our method in three complementary settings. On simulated data with known ground truth, our method detects anatomical change more accurately and consistently than conventional registration. On real image pairs that differ only by GNL distortion, our method assigns most geometric change to the distortion field, demonstrating specificity in the absence of anatomical change. On longitudinal Alzheimer's disease (AD) pairs, our method detects anatomical change in AD-related brain structures while identifying residual distortion left after standard correction. By disentangling MRI-induced distortion from biological change in the longitudinal deformation, our method paves the way for more accurate longitudinal morphometry in clinical settings where maintaining acquisition consistency is challenging.

Jingru Fu, Kathleen E. Larson, Douglas N. Greve +2

Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, USA · Department of Radiology, Massachusetts General Hospital, Boston, USA · Department of Radiology, Harvard Medical School, Boston, USA

Longitudinal Medical Image Analysis Medical Image Registration Magnetic Resonance Imaging Deformable Image Registration Brain MRI