TissUnet: Improved Extracranial Tissue and Cranium Segmentation for Children through Adulthood

Extracranial tissues visible on brain magnetic resonance imaging (MRI) may hold significant value for characterizing health conditions and clinical decision-making, yet they are rarely quantified. Current tools have not been widely validated, particularly in settings of developing brains or underlying pathology. We present TissUnet, a deep learning model that segments skull bone, subcutaneous fat, and muscle from routine three-dimensional T1-weighted MRI, with or without contrast enhancement. The model was trained on 155 paired MRI-computed tomography (CT) scans and validated across nine datasets covering a wide age range and including individuals with brain tumors. In comparison to AI-CT-derived labels from 37 MRI-CT pairs, TissUnet achieved a median Dice coefficient of 0.79 [IQR: 0.77-0.81] in a healthy adult cohort. In a second validation using expert manual annotations, median Dice was 0.83 [IQR: 0.83-0.84] in healthy individuals and 0.81 [IQR: 0.78-0.83] in tumor cases, outperforming previous state-of-the-art method. Acceptability testing resulted in an 89% acceptance rate after adjudication by a tie-breaker(N=108 MRIs), and TissUnet demonstrated excellent performance in the blinded comparative review (N=45 MRIs), including both healthy and tumor cases in pediatric populations. TissUnet enables fast, accurate, and reproducible segmentation of extracranial tissues, supporting large-scale studies on craniofacial morphology, treatment effects, and cardiometabolic risk using standard brain T1w MRI.

Language Models for Automated Classification of Brain MRI Reports and Growth Chart Generation

Clinically acquired brain MRIs and radiology reports are valuable but underutilized resources due to the challenges of manual analysis and data heterogeneity. We developed fine-tuned language models (LMs) to classify brain MRI reports as normal (reports with limited pathology) or abnormal, fine-tuning BERT, BioBERT, ClinicalBERT, and RadBERT on 44,661 reports. We also explored the reasoning capabilities of a leading LM, Gemini 1.5-Pro, for normal report categorization. Automated image processing and modeling generated brain growth charts from LM-classified normal scans, comparing them to human-derived charts. Fine-tuned LMs achieved high classification performance (F1-Score >97%), with unbalanced training mitigating class imbalance. Performance was robust on out-of-distribution data, with full text outperforming summary (impression) sections. Gemini 1.5-Pro showed a promising categorization performance, especially with clinical inference. LM-derived brain growth charts were nearly identical to human-annotated charts (r = 0.99, p < 2.2e-16). Our LMs offer scalable analysis of radiology reports, enabling automated classification of brain MRIs in large datasets. One application is automated generation of brain growth charts for benchmarking quantitative image features. Further research is needed to address data heterogeneity and optimize LM reasoning.