Automated Chest CT Protocol Selection via Large Language Model Derived Text Embeddings from Imaging Request Text

Reasoning in multimodal large language models (MLLMs) has shown strong promise in medical imaging. However, this reasoning is usually free-form text judged only by its final answer, making it hard to interpret and verify, especially in 3D radiology, where a diagnosis should be traceable to evidence in the scan. Existing chest CT question-answering datasets compound this by reducing expert radiology reports to answer-only pairs, dropping the reasoning that links findings to conclusions and omitting the patient history clinicians rely on. As a result, reasoning-capable 3D chest CT MLLMs remain out of reach, as neither the structured supervision needed to train them nor the protocol needed to verify their reasoning yet exists. We introduce CORTEX (Clinically Organized Reasoning and sTructured EXplanation), a structured reasoning benchmark for 3D chest CT. For each question, CORTEX restores the missing reasoning as a four-stage diagnostic trace mirroring a radiologist's workflow: task understanding, visual observation, diagnostic reasoning, and answer synthesis. We generate these traces using frontier large language models with broad medical and general-domain knowledge, then filter and verify them with a stage-level evaluation protocol combining automated rubric scoring with expert radiologist review. Crucially, both the reasoning structure and evaluation rubrics are designed in close collaboration with clinicians. Built on CT-RATE, a large, publicly available chest CT dataset without reasoning annotations, CORTEX comprises 76,177 validated reasoning traces across open-ended VQA, closed-ended VQA, and report generation, providing both the structured supervision and the stage-level evaluation protocol needed to build and evaluate trustworthy reasoning models for 3D chest CT. Our dataset and evaluation code is available at https://huggingface.co/datasets/aneesurhashmi/cortex

Purpose: To evaluate whether large language model (LLM)-assisted label cleaning can identify label-report discordance in CT-RATE, a large-scale public chest CT dataset. Materials and Methods: After report-level deduplication, 24,446 unique radiology reports were identified. Twelve reports were excluded from the primary GPT-5.4 analysis because of Microsoft Azure AI Foundry content-safety filtering, leaving 24,434 reports and 439,812 label instances across 18 abnormality categories. GPT-5.4-derived binary labels were generated from report text using structured JSON output and compared with existing CT-RATE labels. Discordant instances were adjudicated by radiologists. In addition, 100 randomly sampled reports were manually annotated to compare CT-RATE labels, individual LLM-derived labels, and multi-LLM majority-vote labels against radiologist-annotated reference labels. Results: Overall agreement between GPT-5.4-derived and CT-RATE labels was 96.4%, with Cohen's kappa of 0.884. Lymphadenopathy showed the lowest agreement and kappa. In discordance review, radiologist adjudication supported GPT-5.4-derived labels in 72 of 97 (74.2%) general discordant instances and 91 of 99 (91.9%) targeted lymphadenopathy discordant instances. Against radiologist-annotated reference labels, multi-LLM majority-vote labels achieved the highest label-macro-averaged F1 score and Cohen's kappa. Conclusion: LLM-assisted label cleaning identified clinically meaningful label-report discordance in CT-RATE and may support scalable quality improvement of public imaging datasets. The cleaned dataset will be made publicly available to support future research.

Interpreting quantitative CT biomarkers, such as organ volume and tissue attenuation, requires large-scale healthy reference distributions. However, creating these is challenging because clinical datasets are often heavily enriched with pathology. Here, we develop an evidence-grounded, cross-verified large language model (LLM) ensemble to filter pathological findings from radiology reports, enabling the construction of pathology-reduced cohorts from over 350,000 CT examinations. Five LLMs, first, flag structure-level abnormality candidates grounded in verbatim report evidence and, second, resolve disagreements via cross-verification. Using distribution-aware generalized additive models for location, scale, and shape, we establish comprehensive whole-body reference charts for 106 anatomical structures (volumes and attenuation) across adulthood, accounting for age, sex, contrast enhancement, and acquisition parameters. Longitudinal analyses reveal structure- and contrast-dependent changes distinct from cross-sectional trends. These resources facilitate covariate-adjusted centile scoring from routine CT, supporting standardized quantitative phenotyping, multi-site imaging studies, and scalable opportunistic screening research.