Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2211.14051

Open-Source Skull Reconstruction with MONAI

Jianning Li·André Ferreira·Behrus Puladi·Victor Alves·Michael Kamp·Moon-Sung Kim·Felix Nensa·Jens Kleesiek·Seyed-Ahmad Ahmadi·Jan Egger
View original source ↗Read source document ↗Export metadata ↓

Abstract

We present a deep learning-based approach for skull reconstruction for MONAI, which has been pre-trained on the MUG500+ skull dataset. The implementation follows the MONAI contribution guidelines, hence, it can be easily tried out and used, and extended by MONAI users. The primary goal of this paper lies in the investigation of open-sourcing codes and pre-trained deep learning models under the MONAI framework. Nowadays, open-sourcing software, especially (pre-trained) deep learning models, has become increasingly important. Over the years, medical image analysis experienced a tremendous transformation. Over a decade ago, algorithms had to be implemented and optimized with low-level programming languages, like C or C++, to run in a reasonable time on a desktop PC, which was not as powerful as today's computers. Nowadays, users have high-level scripting languages like Python, and frameworks like PyTorch and TensorFlow, along with a sea of public code repositories at hand. As a result, implementations that had thousands of lines of C or C++ code in the past, can now be scripted with a few lines and in addition executed in a fraction of the time. To put this even on a higher level, the Medical Open Network for Artificial Intelligence (MONAI) framework tailors medical imaging research to an even more convenient process, which can boost and push the whole field. The MONAI framework is a freely available, community-supported, open-source and PyTorch-based framework, that also enables to provide research contributions with pre-trained models to others. Codes and pre-trained weights for skull reconstruction are publicly available at: https://github.com/Project-MONAI/research-contributions/tree/master/SkullRec

Explore related subjects

eess.IVcs.CV

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jianning Li, André Ferreira, Behrus Puladi, Victor Alves, Michael Kamp, Moon-Sung Kim, Felix Nensa, Jens Kleesiek, Seyed-Ahmad Ahmadi, Jan Egger. 2023-06-15. Open-Source Skull Reconstruction with MONAI. https://arxiv.org/abs/2211.14051

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

IViT: A Novel Interpretable Visual Transformer for Skin Disease Detection

The clinical diagnosis of skin diseases is susceptible to interference from inter-class similarity of skin lesions, and over-reliance on clinicians'experience easily leads to subjective bias. Although existing deep learning aided diagnosis methods achieve competitive accuracy, they suffer from the black-box opacity of Vision Transformer (ViT) and poor adaptability to medical few-shot scenarios. Moreover, mainstream explainable algorithms generally face the bottleneck of significant accuracy degradation when improving interpretability. This paper proposes an interpretable ViT (IViT) constrained by Quadratic Programming (QP). The introduced pre-trained transfer learning adapts to few-shot feature extraction. A discrete QP feature selection framework is constructed to screen generic and discriminative features consistent with clinical diagnostic logic. A multi-objective loss function is designed to reduce feature redundancy and optimize activation distribution while preserving classification performance. Experimental results on six standard skin disease datasets show that IViT achieves an accuracy of 93.80%, only 0.21% lower than the baseline, with feature redundancy reduced by 29.5%. Its core activation regions are consistent with clinically concerned lesion areas. The proposed model balances accuracy and interpretability, providing a reliable solution for the clinical deployment of few-shot intelligent skin disease diagnosis.

eess.IV↗
arXiv2026

Automated Distinction of Intimal and Medial Intracranial Arterial Calcification from CT Head

Intracranial arterial calcifications (IACs) are a common finding on clinical non-contrast enhanced head CT scans and are associated with neurovascular disease. Calcifications can occur in the intimal or medial layer of the arterial wall, subtypes that differ in aetiology and may have distinct clinical relevance. These subtypes can be visually distinguished by radiologists based on the shape of the calcifications. We investigate three automated approaches for subtype classification of IAC from head CT-derived segmentation masks: (1) an automated adaptation of the established radiological visual score, (2) a sphericity-based method, and (3) a method based on shape embeddings extracted by a medical shape foundation model. All approaches use the same lightweight classification pipeline on top of the features they compute and are evaluated using 5-fold cross-validation. The three methods achieved comparable performance, with the embedding-based approach yielding the best overall results with a weighted F1 (mean $\pm$ SD) of up to 71.5 $\pm$ 3.7 for a single artery and 59.8 $\pm$ 1.7 for the joint artery classification. Performance was largely preserved when using automated instead of manual IAC segmentation masks, and we found the difference in weighted F1 not significant. Our results show that fully automated IAC subtype quantification from head CT is feasible and remains robust to the use of manual and automated IAC segmentation masks. Code at https://github.com/bjin96/iac-subtyping.

eess.IV↗
arXiv2026

Recasting the Destroy Step of Large Neighborhood Search as Dense Segmentation

Large neighborhood search improves an incumbent by releasing selected variables and repairing the resulting subproblem under a time limit. FOVEA casts variable selection as dense semantic segmentation on a fixed $128\times128$ canvas. A small U-Net reads twelve semantic channels and predicts cell scores, which are decoded into a variable set subject to a fixed variable budget. Family-specific layouts connect the search state to the canvas, while one set of network weights serves four problem families. The FP32 network input occupies $786$\,kB across instance sizes. Our analysis bounds constraint coupling for spatially coherent regions, gives a rank certificate for rounds with zero possible improvement, and bounds the coupling advantage attainable on an expander family. On the tested families and hardware, FOVEA trails the strongest graph encoder at $10^{4}$ variables and overtakes it near $1.5\times10^{4}$; the cost model provides an approximate crossover estimate. At larger sizes, where the graph-encoder baselines exceed device memory, FOVEA reduces the primal integral by $12$ to $16\%$ relative to the best runnable baselines. On the expander family, FOVEA performs comparably to random selection, with a coupling advantage close to one.

eess.IV↗