Simulation of Brain Resection for Cavity Segmentation Using Self-Supervised and Semi-Supervised Learning

Resective surgery may be curative for drug-resistant focal epilepsy, but only 40% to 70% of patients achieve seizure freedom after surgery. Retrospective quantitative analysis could elucidate patterns in resected structures and patient outcomes to improve resective surgery. However, the resection cavity must first be segmented on the postoperative MR image. Convolutional neural networks (CNNs) are the state-of-the-art image segmentation technique, but require large amounts of annotated data for training. Annotation of medical images is a time-consuming process requiring highly-trained raters, and often suffering from high inter-rater variability. Self-supervised learning can be used to generate training instances from unlabeled data. We developed an algorithm to simulate resections on preoperative MR images. We curated a new dataset, EPISURG, comprising 431 postoperative and 269 preoperative MR images from 431 patients who underwent resective surgery. In addition to EPISURG, we used three public datasets comprising 1813 preoperative MR images for training. We trained a 3D CNN on artificially resected images created on the fly during training, using images from 1) EPISURG, 2) public datasets and 3) both. To evaluate trained models, we calculate Dice score (DSC) between model segmentations and 200 manual annotations performed by three human raters. The model trained on data with manual annotations obtained a median (interquartile range) DSC of 65.3 (30.6). The DSC of our best-performing model, trained with no manual annotations, is 81.7 (14.2). For comparison, inter-rater agreement between human annotators was 84.0 (9.9). We demonstrate a training method for CNNs using simulated resection cavities that can accurately segment real resection cavities, without manual annotations

The Effect of Vascular Segmentation Methods on Stereotactic Trajectory Planning for Drug-Resistant Focal Epilepsy: A Retrospective Cohort Study

Background: Stereotactic neurosurgical procedures carry a risk of intracranial hemorrhage, which may result in significant morbidity and mortality. Vascular imaging is crucial for planning stereotactic procedures to prevent conflicts with intracranial vasculature. There is a wide range of vascular imaging methods used for stereoelectroencephalography (SEEG) trajectory planning. Computer-assisted planning (CAP) improves planning time and trajectory metrics. We aimed to quantify the effect of different vascular imaging protocols on CAP trajectories for SEEG. Methods: Ten patients who had undergone SEEG (95 electrodes) following preoperative acquisition of gadolinium-enhanced magnetic resonance imaging (MR + Gad), magnetic resonance angiography and magnetic resonance angiography (MRV + MRA), and digital subtraction catheter angiography (DSA) were identified from a prospectively maintained database. SEEG implantations were planned using CAP using DSA segmentations as the gold standard. Strategies were then recreated using MRV + MRA and MR + Gad to define the “apparent” and “true” risk scores associated with each modality. Vessels of varying diameter were then iteratively removed from the DSA segmentation to identify the size at which all 3 vascular modalities returned the same safety metrics. Results: CAP performed using DSA vessel segmentations resulted in significantly lower “true” risk scores and greater minimum distances from vasculature compared with the “true” risk associated with MR + Gad and MRV + MRA. MRV + MRA and MR + Gad returned similar risk scores to DSA when vessels <2 mm and <4 mm were not considered, respectively. Conclusions: Significant variability in vascular imaging and trajectory planning practices exist for SEEG. CAP performed with MR + Gad or MRV + MRA alone returns “falsely” lower risk scores compared with DSA. It is unclear whether DSA is oversensitive and thus restricting potential trajectories

Machine Learning for Localizing Epileptogenic-Zone in the Temporal Lobe: Quantifying the Value of Multimodal Clinical-Semiology and Imaging Concordance

Background: Epilepsy affects 50 million people worldwide and a third are refractory to medication. If a discrete cerebral focus or network can be identified, neurosurgical resection can be curative. Most excisions are in the temporal-lobe, and are more likely to result in seizure-freedom than extra-temporal resections. However, less than half of patients undergoing surgery become entirely seizure-free. Localizing the epileptogenic-zone and individualized outcome predictions are difficult, requiring detailed evaluations at specialist centers. Methods: We used bespoke natural language processing to text-mine 3,800 electronic health records, from 309 epilepsy surgery patients, evaluated over a decade, of whom 126 remained entirely seizure-free. We investigated the diagnostic performances of machine learning models using set-of-semiology (SoS) with and without hippocampal sclerosis (HS) on MRI as features, using STARD criteria. Findings: Support Vector Classifiers (SVC) and Gradient Boosted (GB) decision trees were the best performing algorithms for temporal-lobe epileptogenic zone localization (cross-validated Matthews correlation coefficient (MCC) SVC 0.73 ± 0.25, balanced accuracy 0.81 ± 0.14, AUC 0.95 ± 0.05). Models that only used seizure semiology were not always better than internal benchmarks. The combination of multimodal features, however, enhanced performance metrics including MCC and normalized mutual information (NMI) compared to either alone (p < 0.0001). This combination of semiology and HS on MRI increased both cross-validated MCC and NMI by over 25% (NMI, SVC SoS: 0.35 ± 0.28 vs. SVC SoS+HS: 0.61 ± 0.27). Interpretation: Machine learning models using only the set of seizure semiology (SoS) cannot unequivocally perform better than benchmarks in temporal epileptogenic-zone localization. However, the combination of SoS with an imaging feature (HS) enhance epileptogenic lobe localization. We quantified this added NMI value to be 25% in absolute terms. Despite good performance in localization, no model was able to predict seizure-freedom better than benchmarks. The methods used are widely applicable, and the performance enhancements by combining other clinical, imaging and neurophysiological features could be similarly quantified. Multicenter studies are required to confirm generalizability. Funding: Wellcome/EPSRC Center for Interventional and Surgical Sciences (WEISS) (203145Z/16/Z)

Comparison of robotic and manual implantation of intracerebral electrodes: a single-centre, single-blinded, randomised controlled trial

There has been a significant rise in robotic trajectory guidance devices that have been utilised for stereotactic neurosurgical procedures. These devices have significant costs and associated learning curves. Previous studies reporting devices usage have not undertaken prospective parallel-group comparisons before their introduction, so the comparative differences are unknown. We study the difference in stereoelectroencephalography electrode implantation time between a robotic trajectory guidance device (iSYS1) and manual frameless implantation (PAD) in patients with drug-refractory focal epilepsy through a single-blinded randomised control parallel-group investigation of SEEG electrode implantation, concordant with CONSORT statement. Thirty-two patients (18 male) completed the trial. The iSYS1 returned significantly shorter median operative time for intracranial bolt insertion, 6.36 min (95% CI 5.72–7.07) versus 9.06 min (95% CI 8.16–10.06), p = 0.0001. The PAD group had a better median target point accuracy 1.58 mm (95% CI 1.38–1.82) versus 1.16 mm (95% CI 1.01–1.33), p = 0.004. The mean electrode implantation angle error was 2.13° for the iSYS1 group and 1.71° for the PAD groups (p = 0.023). There was no statistically significant difference for any other outcome. Health policy and hospital commissioners should consider these differences in the context of the opportunity cost of introducing robotic devices

A generative model of hyperelastic strain energy density functions for multiple tissue brain deformation

PURPOSE: Estimation of brain deformation is crucial during neurosurgery. Whilst mechanical characterisation captures stress-strain relationships of tissue, biomechanical models are limited by experimental conditions. This results in variability reported in the literature. The aim of this work was to demonstrate a generative model of strain energy density functions can estimate the elastic properties of tissue using observed brain deformation. METHODS: For the generative model a Gaussian Process regression learns elastic potentials from 73 manuscripts. We evaluate the use of neo-Hookean, Mooney-Rivlin and 1-term Ogden meta-models to guarantee stability. Single and multiple tissue experiments validate the ability of our generative model to estimate tissue properties on a synthetic brain model and in eight temporal lobe resection cases where deformation is observed between pre- and post-operative images. RESULTS: Estimated parameters on a synthetic model are close to the known reference with a root-mean-square error (RMSE) of 0.1 mm and 0.2 mm between surface nodes for single and multiple tissue experiments. In clinical cases, we were able to recover brain deformation from pre- to post-operative images reducing RMSE of differences from 1.37 to 1.08 mm on the ventricle surface and from 5.89 to 4.84 mm on the resection cavity surface. CONCLUSION: Our generative model can capture uncertainties related to mechanical characterisation of tissue. When fitting samples from elastography and linear studies, all meta-models performed similarly. The Ogden meta-model performed the best on hyperelastic studies. We were able to predict elastic parameters in a reference model on a synthetic phantom. However, deformation observed in clinical cases is only partly explained using our generative model

Automated trajectory planning for laser interstitial thermal therapy in mesial temporal lobe epilepsy

OBJECTIVE: Surgical resection of the mesial temporal structures brings seizure remission in 65% of individuals with drug-resistant mesial temporal lobe epilepsy (MTLE). Laser interstitial thermal therapy (LiTT) is a novel therapy that may provide a minimally invasive means of ablating the mesial temporal structures with similar outcomes, while minimizing damage to the neocortex. Systematic trajectory planning helps ensure safety and optimal seizure freedom through adequate ablation of the amygdalohippocampal complex (AHC). Previous studies have highlighted the relationship between the residual unablated mesial hippocampal head and failure to achieve seizure freedom. We aim to implement computer-assisted planning (CAP) to improve the ablation volume and safety of LiTT trajectories. METHODS: Twenty-five patients who had previously undergone LiTT for MTLE were studied retrospectively. The EpiNav platform was used to automatically generate an optimal ablation trajectory, which was compared with the previous manually planned and implemented trajectory. Expected ablation volumes and safety profiles of each trajectory were modeled. The implemented laser trajectory and achieved ablation of mesial temporal lobe structures were quantified and correlated with seizure outcome. RESULTS: CAP automatically generated feasible trajectories with reduced overall risk metrics (P < .001) and intracerebral length (P = .007). There was a significant correlation between the actual and retrospective CAP-anticipated ablation volumes, supporting a 15 mm diameter ablation zone model (P < .001). CAP trajectories would have provided significantly greater ablation of the amygdala (P = .0004) and AHC (P = .008), resulting in less residual unablated mesial hippocampal head (P = .001), and reduced ablation of the parahippocampal gyrus (P = .02). SIGNIFICANCE: Compared to manually planned trajectories CAP provides a better safety profile, with potentially improved seizure-free outcome and reduced neuropsychological deficits, following LiTT for MTLE

Automated multiple trajectory planning algorithm for the placement of stereo-electroencephalography (SEEG) electrodes in epilepsy treatment.

PURPOSE: About one-third of individuals with focal epilepsy continue to have seizures despite optimal medical management. These patients are potentially curable with neurosurgery if the epileptogenic zone (EZ) can be identified and resected. Stereo-electroencephalography (SEEG) to record epileptic activity with intracranial depth electrodes may be required to identify the EZ. Each SEEG electrode trajectory, the path between the entry on the skull and the cerebral target, must be planned carefully to avoid trauma to blood vessels and conflicts between electrodes. In current clinical practice trajectories are determined manually, typically taking 2-3 h per patient (15 min per electrode). Manual planning (MP) aims to achieve an implantation plan with good coverage of the putative EZ, an optimal spatial resolution, and 3D distribution of electrodes. Computer-assisted planning tools can reduce planning time by quantifying trajectory suitability. METHODS: We present an automated multiple trajectory planning (MTP) algorithm to compute implantation plans. MTP uses dynamic programming to determine a set of plans. From this set a depth-first search algorithm finds a suitable plan. We compared our MTP algorithm to (a) MP and (b) an automated single trajectory planning (STP) algorithm on 18 patient plans containing 165 electrodes. RESULTS: MTP changed all 165 trajectories compared to MP. Changes resulted in lower risk (122), increased grey matter sampling (99), shorter length (92), and surgically preferred entry angles (113). MTP changed 42 % (69/165) trajectories compared to STP. Every plan had between 1 to 8 (median 3.5) trajectories changed to resolve electrode conflicts, resulting in surgically preferred plans. CONCLUSION: MTP is computationally efficient, determining implantation plans containing 7-12 electrodes within 1 min, compared to 2-3 h for MP

'Moving life stories tell us just why politics matters’: personal narratives in tabloid anti-austerity campaigns

This article examines the use of personal narratives in two tabloid newspaper campaigns against a controversial welfare reform popularly known as the ‘bedroom tax’. It aims firstly to evaluate whether the personal narratives operate as political testimony to challenge government accounts of welfare reform and dominant stereotypes of benefits claimants, and secondly to assess the potential for and limits to progressive advocacy in popular journalism. The study uses content analysis of 473 articles over the course of a year in the Daily Mirror and Sunday People newspapers, and qualitative analysis of a sub-set of 113 articles to analyse the extent to which the campaign articles extrapolated from the personal to the general, and the role of ‘victim-witnesses’ in articulating their own subjectivity and political agency. The analysis indicates that both newspapers allowed affected individuals to express their own subjectivity to challenge stereotypes, but it was civil society organisations and opinion columnists who most explicitly extrapolated from the personal to the political. Collectively organised benefits claimants were rarely quoted, and there was some evidence of ventriloquization of the editorial voice in the political criticisms of victim-witnesses. However, a campaigning columnist in the Mirror more actively empowered some of those affected to speak directly to politicians. This indicates the value of campaigning journalism when it is truly engaged in solidarity with those affected, rather than instrumentalising victim-witnesses to further the newspapers’ campaign goals

A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections

PURPOSE: Accurate segmentation of brain resection cavities (RCs) aids in postoperative analysis and determining follow-up treatment. Convolutional neural networks (CNNs) are the state-of-the-art image segmentation technique, but require large annotated datasets for training. Annotation of 3D medical images is time-consuming, requires highly trained raters and may suffer from high inter-rater variability. Self-supervised learning strategies can leverage unlabeled data for training. METHODS: We developed an algorithm to simulate resections from preoperative magnetic resonance images (MRIs). We performed self-supervised training of a 3D CNN for RC segmentation using our simulation method. We curated EPISURG, a dataset comprising 430 postoperative and 268 preoperative MRIs from 430 refractory epilepsy patients who underwent resective neurosurgery. We fine-tuned our model on three small annotated datasets from different institutions and on the annotated images in EPISURG, comprising 20, 33, 19 and 133 subjects. RESULTS: The model trained on data with simulated resections obtained median (interquartile range) Dice score coefficients (DSCs) of 81.7 (16.4), 82.4 (36.4), 74.9 (24.2) and 80.5 (18.7) for each of the four datasets. After fine-tuning, DSCs were 89.2 (13.3), 84.1 (19.8), 80.2 (20.1) and 85.2 (10.8). For comparison, inter-rater agreement between human annotators from our previous study was 84.0 (9.9). CONCLUSION: We present a self-supervised learning strategy for 3D CNNs using simulated RCs to accurately segment real RCs on postoperative MRI. Our method generalizes well to data from different institutions, pathologies and modalities. Source code, segmentation models and the EPISURG dataset are available at https://github.com/fepegar/resseg-ijcars

Improving patient safety during introduction of novel medical devices through cumulative summation analysis

Objective: To implement cumulative summation analysis (CUSUM) as an early warning detection and quality assurance system for the pre-clinical testing of the iSYS1 novel robotic trajectory guidance system. Methods: Anatomically accurate 3D printed skull phantoms were created for three patients that had previously undergone implantation of 21 stereoelectroencephalography (SEEG) electrodes using the current standard of care (frameless technique). Implantation schema were recreated using the iSYS1 system and paired accuracy measures were compared with the previous frameless implantations. Entry point, target point and implantation angle accuracy were measured from post-implantation CT scans. CUSUM analysis was undertaken prospectively. Results: The iSYS1 trajectory guidance system significantly improved electrode entry point accuracies from 1.90+/-0.96 mm (Mean+/-SD) to 0.76+/-0.57 mm (Mean+/-SD) without increasing implantation risk. CUSUM analysis was successful as a continuous measure of surgical performance and acted as an early warning detection system. The surgical learning curve, although minimal, showed improvement after insertion of the 8th electrode. Conclusions: The iSYS1 trajectory guidance system did not show any increased risk during phantom preclinical testing when performed by neurosurgeons who had no previous experience of its use. CUSUM analysis is a simple technique that can be applied to all stages of the IDEAL framework as an extra patient safety mechanism. Further clinical trials are required to prove the efficacy of the device