arXiv subjects

Oliver Burgert

Publications and source records attributed to Oliver Burgert.

6 recordsLinked to original sources

arXiv2025

Current validation practice undermines surgical AI development

Surgical data science (SDS) is rapidly advancing, yet clinical adoption of artificial intelligence (AI) in surgery remains limited, with inadequate validation as an important contributing factor. Existing validation practices often neglect the temporal and hierarchical structure of intraoperative videos, yielding misleading or clinically irrelevant results. We introduce a comprehensive catalogue of validation pitfalls in AI-based surgical video analysis, derived from a multi-stage Delphi process with 92 international experts. Pitfalls span three categories: (1) data, (2) metric selection/configuration, and (3) aggregation and reporting. A systematic review of surgical AI papers reveals that these pitfalls are widespread. Experiments on surgical video datasets show that ignoring temporal and hierarchical data structures can understate uncertainty, obscure critical failure modes, and alter algorithm rankings. To address these shortcomings, we provide consensus-based best practices compiled. Together, this work provides an evidence-based framework for rigorous validation of surgical video analysis algorithms, guiding benchmarking, reporting, regulatory review, and clinical translation.

q-bio.OT↗

arXiv2024

The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. Quantitative evaluation and ranking were based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency analysis, and test-time instance optimization per-case basis as a post-processing step. The top-ranked method attained the MEE at or below that of the inter-rater variability for approximately 60% of the evaluated landmarks, underscoring the scope for further accuracy and robustness improvements, especially relative to human experts. The aim of BraTS-Reg is to continue to serve as an active resource for research, with the data and online evaluation tools accessible at https://bratsreg.github.io/.

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arXiv2022

Multimodal CNN Networks for Brain Tumor Segmentation in MRI: A BraTS 2022 Challenge Solution

Automatic segmentation is essential for the brain tumor diagnosis, disease prognosis, and follow-up therapy of patients with gliomas. Still, accurate detection of gliomas and their sub-regions in multimodal MRI is very challenging due to the variety of scanners and imaging protocols. Over the last years, the BraTS Challenge has provided a large number of multi-institutional MRI scans as a benchmark for glioma segmentation algorithms. This paper describes our contribution to the BraTS 2022 Continuous Evaluation challenge. We propose a new ensemble of multiple deep learning frameworks namely, DeepSeg, nnU-Net, and DeepSCAN for automatic glioma boundaries detection in pre-operative MRI. It is worth noting that our ensemble models took first place in the final evaluation on the BraTS testing dataset with Dice scores of 0.9294, 0.8788, and 0.8803, and Hausdorf distance of 5.23, 13.54, and 12.05, for the whole tumor, tumor core, and enhancing tumor, respectively. Furthermore, the proposed ensemble method ranked first in the final ranking on another unseen test dataset, namely Sub-Saharan Africa dataset, achieving mean Dice scores of 0.9737, 0.9593, and 0.9022, and HD95 of 2.66, 1.72, 3.32 for the whole tumor, tumor core, and enhancing tumor, respectively. The docker image for the winning submission is publicly available at (https://hub.docker.com/r/razeineldin/camed22).

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arXiv2022

Self-supervised iRegNet for the Registration of Longitudinal Brain MRI of Diffuse Glioma Patients

Reliable and accurate registration of patient-specific brain magnetic resonance imaging (MRI) scans containing pathologies is challenging due to tissue appearance changes. This paper describes our contribution to the Registration of the longitudinal brain MRI task of the Brain Tumor Sequence Registration Challenge 2022 (BraTS-Reg 2022). We developed an enhanced unsupervised learning-based method that extends the iRegNet. In particular, incorporating an unsupervised learning-based paradigm as well as several minor modifications to the network pipeline, allows the enhanced iRegNet method to achieve respectable results. Experimental findings show that the enhanced self-supervised model is able to improve the initial mean median registration absolute error (MAE) from 8.20 (7.62) mm to the lowest value of 3.51 (3.50) for the training set while achieving an MAE of 2.93 (1.63) mm for the validation set. Additional qualitative validation of this study was conducted through overlaying pre-post MRI pairs before and after the de-formable registration. The proposed method scored 5th place during the testing phase of the MICCAI BraTS-Reg 2022 challenge. The docker image to reproduce our BraTS-Reg submission results will be publicly available.

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arXiv2021

Ensemble CNN Networks for GBM Tumors Segmentation using Multi-parametric MRI

Glioblastomas are the most aggressive fast-growing primary brain cancer which originate in the glial cells of the brain. Accurate identification of the malignant brain tumor and its sub-regions is still one of the most challenging problems in medical image segmentation. The Brain Tumor Segmentation Challenge (BraTS) has been a popular benchmark for automatic brain glioblastomas segmentation algorithms since its initiation. In this year, BraTS 2021 challenge provides the largest multi-parametric (mpMRI) dataset of 2,000 pre-operative patients. In this paper, we propose a new aggregation of two deep learning frameworks namely, DeepSeg and nnU-Net for automatic glioblastoma recognition in pre-operative mpMRI. Our ensemble method obtains Dice similarity scores of 92.00, 87.33, and 84.10 and Hausdorff Distances of 3.81, 8.91, and 16.02 for the enhancing tumor, tumor core, and whole tumor regions, respectively, on the BraTS 2021 validation set, ranking us among the top ten teams. These experimental findings provide evidence that it can be readily applied clinically and thereby aiding in the brain cancer prognosis, therapy planning, and therapy response monitoring. A docker image for reproducing our segmentation results is available online at (https://hub.docker.com/r/razeineldin/deepseg21).

cs.CV↗

arXiv2020

DeepSeg: Deep Neural Network Framework for Automatic Brain Tumor Segmentation using Magnetic Resonance FLAIR Images

Purpose: Gliomas are the most common and aggressive type of brain tumors due to their infiltrative nature and rapid progression. The process of distinguishing tumor boundaries from healthy cells is still a challenging task in the clinical routine. Fluid-Attenuated Inversion Recovery (FLAIR) MRI modality can provide the physician with information about tumor infiltration. Therefore, this paper proposes a new generic deep learning architecture; namely DeepSeg for fully automated detection and segmentation of the brain lesion using FLAIR MRI data. Methods: The developed DeepSeg is a modular decoupling framework. It consists of two connected core parts based on an encoding and decoding relationship. The encoder part is a convolutional neural network (CNN) responsible for spatial information extraction. The resulting semantic map is inserted into the decoder part to get the full resolution probability map. Based on modified U-Net architecture, different CNN models such as Residual Neural Network (ResNet), Dense Convolutional Network (DenseNet), and NASNet have been utilized in this study. Results: The proposed deep learning architectures have been successfully tested and evaluated on-line based on MRI datasets of Brain Tumor Segmentation (BraTS 2019) challenge, including s336 cases as training data and 125 cases for validation data. The dice and Hausdorff distance scores of obtained segmentation results are about 0.81 to 0.84 and 9.8 to 19.7 correspondingly. Conclusion: This study showed successful feasibility and comparative performance of applying different deep learning models in a new DeepSeg framework for automated brain tumor segmentation in FLAIR MR images. The proposed DeepSeg is open-source and freely available at https://github.com/razeineldin/DeepSeg/.

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