arXiv subjects

Necati Sefercioglu

Publications and source records attributed to Necati Sefercioglu.

2 recordsLinked to original sources

arXiv2026

Measure Before You Repair: An Explainable Agent for Blind Restoration of Multi-Artifact 3-D MRI

A brain MRI scan can carry an unknown mix of artifacts, so restoration has to be blind, yet most deep-learning methods are built to correct one known artifact. We present Dx-Rx, an agent in which a multimodal large language model (MLLM) measures suspected artifacts before it repairs them. To our knowledge, it is the first agent to restore whole 3-D MRI volumes, whereas earlier MRI agents restore 2-D slices. In a loop, it looks at slices of the 3-D volume, calls five diagnostic tools (noise, spike, ghosting, bias field, motion) and four restoration tools in any order it chooses, checks each repair, can return to any earlier version to change the order, and ends with a radiology-style report of its diagnostic reasons, the repairs it applied and their results. We simulated up to five artifacts on 148 whole 3-D T1-weighted volumes, at levels calibrated to radiologists' grades of real scans. An MLLM that only looked at the image, as earlier MRI agents do, removed at most 19.7 % of the artifact error. With the best of five MLLMs, Dx-Rx removed a mean 64.5 %, nearly matching the 64.6 % of the same tools given the ground-truth artifacts, which are never known for a clinical scan. With all five models, it made no volume worse and was on par with or better than an expert rule-based pipeline built from the same tools (62.3 %). Code and demo are public at https://itu-biai.github.io/measure-before-you-repair.

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arXiv2025

Task-Adaptive Low-Dose CT Reconstruction

Deep learning-based low-dose computed tomography reconstruction methods already achieve high performance on standard image quality metrics like peak signal-to-noise ratio and structural similarity index measure. Yet, they frequently fail to preserve the critical anatomical details needed for diagnostic tasks. This fundamental limitation hinders their clinical applicability despite their high metric scores. We propose a novel task-adaptive reconstruction framework that addresses this gap by incorporating a frozen pre-trained task network as a regularization term in the reconstruction loss function. Unlike existing joint-training approaches that simultaneously optimize both reconstruction and task networks, and risk diverging from satisfactory reconstructions, our method leverages a pre-trained task model to guide reconstruction training while still maintaining diagnostic quality. We validate our framework on a liver and liver tumor segmentation task. Our task-adaptive models achieve Dice scores up to 0.707, approaching the performance of full-dose scans (0.874), and substantially outperforming joint-training approaches (0.331) and traditional reconstruction methods (0.626). Critically, our framework can be integrated into any existing deep learning-based reconstruction model through simple loss function modification, enabling widespread adoption for task-adaptive optimization in clinical practice. Our codes are available at: https://github.com/itu-biai/task_adaptive_ct

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