Artificial Intelligence for the Detection of Focal Cortical Dysplasia: Challenges in Translating Algorithms into Clinical Practice

Focal cortical dysplasias (FCDs) are malformations of cortical development and one of the most common pathologies causing pharmacoresistant focal epilepsy. Resective neurosurgery yields high success rates, especially if the full extent of the lesion is correctly identified and completely removed. The visual assessment of magnetic resonance imaging does not pinpoint the FCD in 30%–50% of cases, and half of all patients with FCD are not amenable to epilepsy surgery, partly because the FCD could not be sufficiently localized. Computational approaches to FCD detection are an active area of research, benefitting from advancements in computer vision. Automatic FCD detection is a significant challenge and one of the first clinical grounds where the application of artificial intelligence may translate into an advance for patients' health. The emergence of new methods from the combination of health and computer sciences creates novel challenges. Imaging data need to be organized into structured, well-annotated datasets and combined with other clinical information, such as histopathological subtypes or neuroimaging characteristics. Algorithmic output, that is, model prediction, requires a technically correct evaluation with adequate metrics that are understandable and usable for clinicians. Publication of code and data is necessary to make research accessible and reproducible. This critical review introduces the field of automatic FCD detection, explaining underlying medical and technical concepts, highlighting its challenges and current limitations, and providing a perspective for a novel research environment

Multiple classifier fusion and optimization for automatic focal cortical dysplasia detection on magnetic resonance images

In magnetic resonance (MR) images, detection of focal cortical dysplasia (FCD) lesion as a main pathological cue of epilepsy is challenging because of the variability in the presentation of FCD lesions. Existing algorithms appear to have sufficient sensitivity in detecting lesions but also generate large numbers of false-positive (FP) results. In this paper, we propose a multiple classifier fusion and optimization schemes to automatically detect FCD lesions in MR images with reduced FPs through constructing an objective function based on the F-score. Thus, the proposed scheme obtains an improved tradeoff between minimizing FPs and maximizing true positives. The optimization is achieved by incorporating the genetic algorithm into the work scheme. Hence, the contribution of weighting coefficients to different classifications can be effectively determined. The resultant optimized weightings are applied to fuse the classification results. A set of six typical FCD features and six corresponding Z-score maps are evaluated through the mean F-score from multiple classifiers for each feature. From the experimental results, the proposed scheme can automatically detect FCD lesions in 9 out of 10 patients while correctly classifying 31 healthy controls. The proposed scheme acquires a lower FP rate and a higher F-score in comparison with two state-of-the-art methods

Advanced Magnetic Resonance Imaging and Quantitative Analysis Approaches in Patients with Refractory Focal Epilepsy

Background Epilepsy has a high prevalence of 1%, which makes it the most common serious neurological disorder. The most difficult to treat type of epilepsy is temporal lobe epilepsy (TLE) with its most commonly associated lesion being hippocampal sclerosis (HS). About 30-50% of all patients undergoing resective surgery of epileptogenic tissue continue to have seizures postoperatively. Indication for this type of surgery is only given when lesions are clearly visible on magnetic resonance images (MRI). About 30% of all patients with focal epilepsy do not show an underlying structural lesion upon qualitative neuroradiological MRI assessment (MRI-negative). Objectives The work presented in this thesis uses MRI data to quantitatively investigate structural differences between brains of patients with focal epilepsy and healthy controls using automated imaging preprocessing and analysis methods. Methods All patients studied in this thesis had electrophysiological evidence of focal epilepsy, and underwent routine clinical MRI prior to participation in this study. There were two datasets and both included a cohort of age-matched controls: (i) Patients with TLE and associated HS who later underwent selective amygdalahippocampectomy (cohort 1) and (ii) MRI-negative patients with medically refractory focal epilepsy (cohort 2). The participants received high- resolution routine clinical MRI as well as additional sequences for gray and white matter (GM/WM) structural imaging. A neuroradiologist reviewed all images prior to analysis. Hippocampal subfield volume and automated tractography analysis was performed in patients with TLE and HS and related to post-surgical outcomes, while images of MRI- negative patients were analyzed using voxel-based morphometry (VBM) and manual/automated tractography. All studies were designed to detect quantitative differences between patients and controls, except for the hippocampal subfield analysis as control data was not available and comparisons were limited to patients with persistent postoperative seizures and those without. Results 1. Automated hippocampal subfield analysis (cohort 1): The high-resolution hippocampal subfield segmentation technique cannot establish a link between hippocampal subfield volume loss and post-surgical outcome. Ipsilateral and contralateral hippocampal subfield volumes did not correlate with clinical variables such as duration of epilepsy and age of onset of epilepsy. 2. Automated WM diffusivity analysis (cohort 1): Along-the-tract analysis showed that ipsilateral tracts of patients with right/left TLE and HS were more extensively affected than contralateral tracts and the affected regions within tracts could be specified. The extent of hippocampal atrophy (HA) was not related to (i) the diffusion alterations of temporal lobe tracts or (ii) clinical characteristics of patients, whereas diffusion alterations of ipsilateral temporal lobe tracts were significantly related to age at onset of epilepsy, duration of epilepsy and epilepsy burden.Patients without any postoperative seizure symptoms (excellent outcomes) had more ipsilaterally distributed WM tract diffusion alterations than patients with persistent postoperative seizures (poorer outcomes), who were affected bilaterally. 3. Automated epileptogenic lesion detection (cohort 2): Comparison of individual patients against the controls revealed that focal cortical dysplasia (FCD) can be detected automatically using statistical thresholds. All sites of dysplasia reported at the start of the study were detected using this technique. Two additional sites in two different patients, which had previously escaped neuroradiological assessment, could be identified. When taking these statistical results into account during re-assessment of the dedicated epilepsy research MRI, the expert neuroradiologist was able to confirm these as lesions. 4. Manual and automated WM diffusion tensor imaging (DTI) analysis (cohort 2): The analysis of consistency across approaches revealed a moderate to good agreement between extracted tract shape, morphology and space and a strong correlation between diffusion values extracted with both methods. While whole-tract DTI-metrics determined using Automated Fiber Quantification (AFQ) revealed correlations with clinical variables such as age of onset and duration of epilepsy, these correlations were not found using the manual technique. The manual approach revealed more differences than AFQ in group comparisons of whole-tract DTI-metrics. Along-the-tract analysis provided within AFQ gave a more detailed description of localized diffusivity changes along tracts, which correlated with clinical variables such as age of onset and epilepsy duration. Conclusions While hippocampal subfield volume loss in patients with TLE and HS was not related with any clinical variables or to post-surgical outcomes, WM tract diffusion alterations were more bilaterally distributed in patients with persistent postoperative seizures, compared to patients with excellent outcomes. This may indicate that HS as an initial precipitating injury is not affected by clinical features of the disorder and automated hippocampal subfield mapping based on MRI is not sufficient to stratify patients according to outcome. Presence of persisting seizures may depend on other pathological processes such as seizure propagation through WM tracts and WM integrity. Automated and time-efficient three-dimensional voxel-based analysis may complement conventional visual assessments in patients with MRI-negative focal epilepsy and help to identify FCDs escaping routine neuroradiological assessment. Furthermore, automated along-the-tract analysis may identify widespread abnormal diffusivity and correlations between WM integrity loss and clinical variables in patients with MRI-negative epilepsy. However, automated WM tract analysis may differ from results obtained with manual methods and therefore caution should be exercised when using automated techniques

Histological Quantification in Temporal Lobe Epilepsy

Approximately 30 percent of epilepsy patients suffer from refractory temporal lobe epilepsy which is commonly treated with resection of the epileptogenic tissue. However, surgical treatment presents many challenges in locating the epileptogenic focus and thus not all patients become seizure-free following surgery. Advances in techniques can lead to improved localization of the epileptogenic zone and may be validated by correlating MRI with neuropathology of the excised cortical tissue. Focal cortical dysplasias are a neuropathological group of cortical malformations that are often found in cases of refractory epilepsy, however, they are subtle and difficult to quantify. The purpose of this research is to employ histology image analysis techniques to better characterize these abnormalities at the neuronal and laminar level, allowing for correlative MRI-histology studies and improved lesion detection in medically intractable TLE

Cortical Morphology and MRI Signal Intensity Analysis in Paediatric Epilepsy

Epilepsy encompasses a great variety of aetiologies, and as such is not a single disease but a group of diseases characterised by unprovoked seizures.The primary aim of the work presented in this thesis was to use multimodal structural imaging to improve understanding of epilepsy related brain pathology, both the epileptogenic lesions themselves and extralesional pathology, in order to improve pre-surgical planning in medicationresistant epilepsy and improve understanding of the underlying pathogenic mechanisms. The work focuses on 2 epilepsy aetiologies: focal cortical dysplasia (FCD) (chapters 2 and 3) and mesial temporal lobe epilepsy (chapters 4 & 5). Chapter 2 of this thesis develops surface-based, structural MRI post-processing techniques that can be applied to clinical T1 and FLAIR images to complement current MRI-based diagnosis of focal cortical dysplasias. Chapter 3 uses the features developed in Chapter 2 within a machine learning framework to automatically detect FCDs, obtaining 73% sensitivity using a neural network. Chapter 4 develops an in vivo method to explore neocortical gliosis in adults with TLE, while Chapter 5 applies this method to a paediatric cohort. Finally, the concluding chapter discusses contributions, main limitations and outlines options for future research

Gray-matter-specific MR imaging improves the detection of epileptogenic zones in focal cortical dysplasia: A new sequence called fluid and white matter suppression (FLAWS).

To evaluate the diagnostic value and characteristic features of FCD epileptogenic zones using a novel sequence called fluid and white matter suppression (FLAWS). Thirty-nine patients with pathologically confirmed FCD and good surgery outcomes (class I or II, according to the Engel Epilepsy Surgery Outcome Scale) were retrospectively included in the study. All the patients underwent a preoperative whole-brain MRI examination that included conventional sequences (T2WI, T1WI, two-dimensional (2D) axial, coronal fluid-attenuated inversion recovery [FLAIR]) and FLAWS. An additional 3D-FLAIR MRI sequence was performed in 17 patients. To evaluate the sensitivity and specificity of FLAWS and investigate the cause of false-positives, 36 healthy volunteers were recruited as normal controls. Two radiologists evaluated all the image data. The detection rates of the FCD epileptogenic zone on different sequences were compared based on five criteria: abnormal cortical morphology (thickening, thinning, or abnormally deep sulcus); abnormal cortical signal intensity; blurred gray-white matter junction; abnormal signal intensity of the subcortical white matter, and the transmantle sign. The sensitivity and specificity of FLAWS for detecting the FCD lesions were calculated with the reviewers blinded to all the clinical information, i.e. to the patient identity and the location of the resected regions. To explore how many features were sufficient for the diagnosis of the epileptogenic zones, the frequency of each criterion in the resected regions and their combinations were assessed on FLAWS, according to the results of the assessment when the reviewers were aware of the location of the resected regions. Based on the findings of the 17 patients with an additional 3D-FLAIR scan when the reviewers were aware of the location of the resected regions, quantitative analysis of the regions of interest was used to compare the tissue contrast among 2D-axial FLAIR, 3D-FLAIR, and the FLAWS sequence. Visualization score analysis was used to evaluate the visualization of the five features on conventional, 3D-FLAIR, and FLAWS images. Finally, to explore the reason for false-positive results, a further evaluation of the whole brain FLAWS images was conducted for all the subjects. The sensitivity and specificity for detecting the FCD lesions on the FLAWS sequence were 71.9% and 71.1%, respectively. When the reviewers were blinded to the location of the resected regions, the detection rate of the FLAWS sequence was significantly higher than that of the conventional sequences (P = 0.00). In the 17 patients who underwent an additional 3D FLAIR scan, no statistically significant difference was found between the FLAWS and the 3D-FLAIR (P = 0.25). All the patients had at least two imaging features, one of which was "the blurred junction of the gray-white matter." The transmantle sign, which is widely believed to be a specific feature of FCD type II, could also be observed in type I on the FLAWS sequence. The relative tissue contrast of FLAWS was higher than that of the 2D-FLAIR with respect to lesion/white matter (WM), deep gray matter (GM)/WM, and cortex/WM (P = 0.00 for all three measures) and higher than that of the 3D-FLAIR with respect to the lesion/WM (P = 0.01). The visualization score analysis showed that the visualization of FLAWS was more enhanced than that of the conventional and 3D-FLAIR images with respect to the blurred junction (P = 0.00 for both comparisons) and the abnormal signal intensity of the subcortical white matter (P = 0.01 for both comparisons). The thin-threadlike signal and individual FCD features outside the epileptogenic regions were considered the primary cause of the false-positive results of FLAWS. FLAWS can help in the detection of FCD epileptogenic zones. It is recommended that epileptogenic zone on FLAWS be diagnosed based on a combination of two features, one of which should be the "blurred junction of the gray-white matter" in types I and II. In type III, the combination of "the blurred junction of the gray-white matter" with "abnormal signal intensity of subcortical white matter" is recommended

Quantitative multi-modal analysis of pediatric focal epilepsy

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 101-103).For patients with medically refractive focal epilepsy, surgical intervention to remove the epileptic foci is often the last alternative for permanent cure. The success of such surgery is highly dependent on the doctor's ability to accurately locate the epileptogenic region during the pre-surgical planning and evaluation phase. Hence the goal of this project is to provide an end-to-end quantitative analysis pipeline that fuses an array of imaging modalities including magnetic resonance imaging (MRI), diffusion tensor MRI, positron emission tomography (PET), single-photon emission computerized tomography (SPECT) as well as EEG data to build patient-specific head models and to compute prior probability maps of epileptic hotspots for more accurate EEG source localization. By improving the ability to accurately locate these epileptogenic seizure sources, patients can benefit tremendously from accurate surgical resection and consequently have a better chance for complete seizure free recovery.by Andy Khai Siang Eow.S.M

Memory Performance in Children with Temporal Lobe Epilepsy: Neocortical vs. Dual Pathologies

This study investigated memory in children with temporal lobe epilepsy and the ability to discern hippocampal dysfunction with conventional memory tests that are typically used to detect more global memory impairment. All data was obtained retrospectively from the epilepsy surgery program at a local children’s hospital. The research population consisted of 54 children with intractable epilepsy of temporal onset, balanced across pathology types (with and without hippocampal disease) and other demographics. Each was given a clinical battery prior to surgical intervention, which included the WRAML/WRAML2 Verbal Learning subtest from which the dependent variables for this study were extracted. The research hypothesis had predicted that memory retention between verbal learning and recall would be worse for participants with pathology that included hippocampal sclerosis than for those with non-hippocampal temporal lobe pathology. A two-way mixed-design ANOVA was used to test the hypothesis, which allowed incorporation of variables of interest related to memory factors, pathology type, and hemispheric laterality, as well as their various interactions. There was a significant main effect for change in the number of words retained from the final learning trial to the delayed recall. Although the interaction between memory retention and pathology type was not statistically significant, the average of the memory scores as it related to pathology by side did show significance. Thus, results did not support the hypothetical relationship between retention and hippocampal function. However, additional exploratory analyses revealed that the final learning trial by itself was associated with hippocampal pathology, which applied only to those participants with left-hemisphere lesions. Logistic regression with the final learning trial correctly classified 74 percent of participants into the appropriate pathology category, with 81 percent sensitivity to hippocampal dysfunction. Mean participant memory scores were nearly one standard deviation below the normative mean for both delayed recall and total learning scaled scores, regardless of pathology type or lesion hemisphericity. Thus, while the conventionally used indices of the WRAML Verbal Learning test are useful for determining overall memory status, they are not specific to pathological substrate. The within-subject main effect showed an expected loss of information across the time of the delay, but overall the recall score showed no association with hippocampal functioning. This study revealed the possibility of measuring hippocampal function at statistically significant group levels using learning scores from a widely used measure of verbal memory, even in participants with intact contralateral mesial temporal structures. It also indicated that hippocampal structures do not play a role during recall measures given after a standard time delay. Data further demonstrated a role of the hippocampus for encoding and transferring information beyond short term/working memory into long term. During the learning process, the hippocampus appears to work in concert with short-term memory systems, but does not take over the encoding process until enough repetitions have occurred to saturate the working memory buffer. This research represents a small, yet important step forward in our understanding of the hippocampus, with potentially important implications for the future study of memory constructs and mensuration