Overcoming challenges of translating deep-learning models for glioblastoma: the ZGBM consortium

Objective: To report imaging protocol and scheduling variance in routine care of glioblastoma patients in order to demonstrate challenges of integrating deep-learning models in glioblastoma care pathways. Additionally, to understand the most common imaging studies and image contrasts to inform the development of potentially robust deep-learning models. Methods: MR imaging data were analysed from a random sample of five patients from the prospective cohort across five participating sites of the ZGBM consortium. Reported clinical and treatment data alongside DICOM header information were analysed to understand treatment pathway imaging schedules. Results: All sites perform all structural imaging at every stage in the pathway except for the presurgical study, where in some sites only contrast-enhanced T1-weighted imaging is performed. Diffusion MRI is the most common non-structural imaging type, performed at every site. Conclusion: The imaging protocol and scheduling varies across the UK, making it challenging to develop machine-learning models that could perform robustly at other centres. Structural imaging is performed most consistently across all centres. Advances in knowledge: Successful translation of deep-learning models will likely be based on structural post-treatment imaging unless there is significant effort made to standardise non-structural or peri-operative imaging protocols and schedules.

Machine Learning and Glioblastoma: Treatment Response Monitoring Biomarkers in 2021

The aim of the systematic review was to assess recently published studies on diagnostic test accuracy of glioblastoma treatment response monitoring biomarkers in adults, developed through machine learning (ML). Articles were searched for using MEDLINE, EMBASE, and the Cochrane Register. Included study participants were adult patients with high grade glioma who had undergone standard treatment (maximal resection, radiotherapy with concomitant and adjuvant temozolomide) and subsequently underwent follow-up imaging to determine treatment response status. Risk of bias and applicability was assessed with QUADAS 2 methodology. Contingency tables were created for hold-out test sets and recall, specificity, precision, F1-score, balanced accuracy calculated. Fifteen studies were included with 1038 patients in training sets and 233 in test sets. To determine whether there was progression or a mimic, the reference standard combination of follow-up imaging and histopathology at re-operation was applied in 67% of studies. The small numbers of patient included in studies, the high risk of bias and concerns of applicability in the study designs (particularly in relation to the reference standard and patient selection due to confounding), and the low level of evidence, suggest that limited conclusions can be drawn from the data. There is likely good diagnostic performance of machine learning models that use MRI features to distinguish between progression and mimics. The diagnostic performance of ML using implicit features did not appear to be superior to ML using explicit features. There are a range of ML-based solutions poised to become treatment response monitoring biomarkers for glioblastoma. To achieve this, the development and validation of ML models require large, well-annotated datasets where the potential for confounding in the study design has been carefully considered.

Using convolution neural networks to learn enhanced fiber orientation distribution models from commercially available diffusion magnetic resonance imaging

Accurate local fiber orientation distribution (FOD) modeling based on diffusion magnetic resonance imaging (dMRI) capable of resolving complex fiber configurations benefit from specific acquisition protocols that impose a high number of gradient directions (b-vecs), a high maximum b-value (b-vals) and multiple b-values (multi-shell). However, acquisition time is limited in a clinical setting and commercial scanners may not provide robust state-of-the-art dMRI sequences. Therefore, dMRI is often acquired as single-shell (SS) (single b-value). Here, we learn improved FODs for commercially acquired dMRI. We evaluate the use of 3D convolutional neural networks (CNNs) to regress multi-shell FOS representations from single-shell representations, using the spherical harmonics basis obtained from constrained spherical deconvolution (CSD) to model FODs. We use U-Net and HighResNet 3D CNN architectures and data from the publicly available Human Connectome Dataset and a dataset acquired at National Hospital For Neurology and Neurosurgery Queen Square. We evaluate how well the CNN models can resolve local fiber orientation 1) when training and testing on datasets with same dMRI acquisition protocol; 2) when testing on dataset with a different dMRI acquisition protocol than used training the CNN models; and 3) when testing on datasets with a fewer number dMRI gradient directions than used training the CNN models. Our approach may enable robust CSD model estimation on dMRI acquisition protocols which are single shell and with a few gradient directions, reducing acquisition times, and thus, facilitating translation to time-limited clinical environments.