Reducing CNN textural bias with k-space artifacts improves robustness

Convolutional neural networks (CNNs) have become the de facto algorithms of choice for semantic segmentation tasks in biomedical image processing. Yet, models based on CNNs remain susceptible to the domain shift problem, where a mismatch between source and target distributions could lead to a drop in performance. CNNs were recently shown to exhibit a textural bias when processing natural images, and recent studies suggest that this bias also extends to the context of biomedical imaging. In this paper, we focus on Magnetic Resonance Images (MRI) and investigate textural bias in the context of k -space artifacts (Gibbs, spike, and wraparound artifacts), which naturally manifest in clinical MRI scans. We show that carefully introducing such artifacts at training time can help reduce textural bias, and consequently lead to CNN models that are more robust to acquisition noise and out-of-distribution inference, including scans from hospitals not seen during training. We also present Gibbs ResUnet; a novel, end-to-end framework that automatically finds an optimal combination of Gibbs k -space stylizations and segmentation model weights. We illustrate our findings on multimodal and multi-institutional clinical MRI datasets obtained retrospectively from the Medical Segmentation Decathlon (n=750) and The Cancer Imaging Archive (n=243)

Radiomics in paediatric neuro-oncology : MRI textural features as diagnostic and prognostic biomarkers

Motivation: Brain and central nervous system tumours form the second most common group of cancers in children in the UK, accounting for 27% of all childhood cancers. Despite current advances in magnetic resonance imaging (MRI), non-invasive characterisation of paediatric brain tumours remains challenging. Radiomics, the high-throughput extraction and analysis of quantitative image features (e.g. texture), offers potential solutions for tumour characterisation and decision support. Aim and Methods: In search for diagnostic and prognostic oncological markers, the aim of this thesis was to study the application of MRI texture analysis (TA) for the characterisation of paediatric brain tumours. To this end, single and multi-centre experiments were carried out, within a supervised classification framework, on clinical MR imaging datasets of common brain tumour types. Results: TA of conventional MRI was successfully used for diagnostic classification of common paediatric brain tumours. A key contribution of this thesis was to provide evidence that diagnostic classification could be optimised by extending the analysis to include three-dimensional features obtained from multiple MR imaging slices. In addition to this, TA was shown to have a good cross-centre transferability, which is essential for long-term clinical adoption of the technique. Finally, fifteen textural features extracted from T2-weighted MRI were identified to be of significant prognostic value for paediatric medulloblastoma. Conclusion: It was shown that MRI TA provides valuable quantifiable information that can supplement qualitative assessments conducted by radiologists, for the characterisation of paediatric brain tumours. TA can potentially have a large clinical impact, since MR imaging is routinely used in the brain cancer clinical work-flow worldwide, providing an opportunity to improve personalised healthcare and decision-support at low cost

Distinguishing between paediatric brain tumour types using multi-parametric magnetic resonance imaging and machine learning: a multi-site study

The imaging and subsequent accurate diagnosis of paediatric brain tumours presents a radiological challenge, with magnetic resonance imaging playing a key role in providing tumour specific imaging information. Diffusion weighted and perfusion imaging are commonly used to aid the non-invasive diagnosis of children's brain tumours, but are usually evaluated by expert qualitative review. Quantitative studies are mainly single centre and single modality. The aim of this work was to combine multi-centre diffusion and perfusion imaging, with machine learning, to develop machine learning based classifiers to discriminate between three common paediatric tumour types. The results show that diffusion and perfusion weighted imaging of both the tumour and whole brain provide significant features which differ between tumour types, and that combining these features gives the optimal machine learning classifier with >80% predictive precision. This work represents a step forward to aid in the non-invasive diagnosis of paediatric brain tumours, using advanced clinical imaging

Metamaterial formalism approach for advancing the recognition of glioma areas in brain tissue biopsies

Early detection of a tumor makes it more probable that the patient will, finally, beat cancer and recover. The main goal of broadly defined cancer diagnostics is to determine whether a patient has a tumor, where it is located, and its histological type and severity. The major characteristic of the cancer affected tissue is the presence of the glioma cells in the sample. The current approach in diagnosis focuses mainly on microbiological, immunological, and pathological aspects rather than on the “metamaterial geometry” of the diseases. The determination of the effective properties of the biological tissue samples and treating them as disordered metamaterial media has become possible with the development of effective medium approximation techniques. Their advantage lies in their capability to treat the biological tissue samples as metamaterial structures, possessing the well-studied properties. Here, we present, for the first time to our knowledge, the studies on metamaterial properties of biological tissues to identify healthy and cancerous areas in the brain tissue. The results show that the metamaterial properties strongly differ depending on the tissue type, if it is healthy or unhealthy. The obtained effective permittivity values were dependent on various factors, like the amount of different cell types in the sample and their distribution. Based on these findings, the identification of the cancer affected areas based on their effective medium properties was performed. These results prove the metamaterial model capability in recognition of the cancer affected areas. The presented approach can have a significant impact on the development of methodological approaches toward precise identification of pathological tissues and would allow for more effective detection of cancer-related changes