Cortical thickness and grey-matter volume anomaly detection in individual MRI scans: Comparison of two methods.

Over the past decades, morphometric analysis of brain MRI has contributed substantially to the understanding of healthy brain structure, development and aging as well as to improved characterisation of disease related pathologies. Certified commercial tools based on normative modeling of these metrics are meanwhile available for diagnostic purposes, but they are cost intensive and their clinical evaluation is still in its infancy. Here we have compared the performance of "ScanOMetrics", an open-source research-level tool for detection of statistical anomalies in individual MRI scans, depending on whether it is operated on the output of FreeSurfer or of the deep learning based brain morphometry tool DL + DiReCT. When applied to the public OASIS3 dataset, containing patients with Alzheimer's disease (AD) and healthy controls (HC), cortical thickness anomalies in patient scans were mainly detected in regions that are known as predilection areas of cortical atrophy in AD, regardless of the software used for extraction of the metrics. By contrast, anomaly detections in HCs were up to twenty-fold reduced and spatially unspecific using both DL + DiReCT and FreeSurfer. Progression of the atrophy pattern with clinical dementia rating (CDR) was clearly observable with both methods. DL + DiReCT provided results in less than 25 min, more than 15 times faster than FreeSurfer. This difference in computation time might be relevant when considering application of this or similar methodology as diagnostic decision support for neuroradiologists.

Transient brain structure changes after high phenylalanine exposure in adults with phenylketonuria.

Phenylketonuria is a rare metabolic disease resulting from a deficiency of the enzyme phenylalanine hydroxylase. Recent cross-sectional evidence suggests that early-treated adults with phenylketonuria exhibit alterations in cortical grey matter compared to healthy peers. However, the effects of high phenylalanine exposure on brain structure in adulthood need to be further elucidated. In this double-blind, randomised, placebo-controlled crossover trial, we investigated the impact of a four-week high phenylalanine exposure on the brain structure and its relationship to cognitive performance and metabolic parameters in early-treated adults with phenylketonuria. Twenty-eight adult patients with early-treated classical phenylketonuria (19-48 years) underwent magnetic resonance imaging before and after the four-week phenylalanine and placebo interventions (four timepoints). Structural T1-weighted images were preprocessed and evaluated using DL+DiReCT, a deep-learning-based tool for brain morphometric analysis. Cortical thickness, white matter volume, and ventricular volume were compared between the phenylalanine and placebo periods. Brain phenylalanine levels were measured using 1H spectroscopy. Blood levels of phenylalanine, tyrosine, and tryptophan were assessed at each of the four timepoints, along with performance in executive functions and attention. Blood phenylalanine levels were significantly higher after the phenylalanine period (1441µmol/L) than after the placebo period (873µmol/L, P<0.001). Morphometric analyses revealed a statistically significant decrease in cortical thickness in 17 out of 60 brain regions after the phenylalanine period compared to placebo. The largest decreases were observed in the right pars orbitalis (point estimate=-0.095mm, P<0.001) and the left lingual gyrus (point estimate=-0.070mm, P<0.001). Bilateral white matter and ventricular volumes were significantly increased after the phenylalanine period. However, the structural alterations in the Phe-placebo group returned to baseline measures following the washout and placebo period. Additionally, elevated blood and brain phenylalanine levels were related to increased bilateral white matter volume (rs=0.43 to 0.51, P≤0.036) and decreased cortical thickness (rs=-0.62 to -0.39, not surviving FDR correction) after the phenylalanine and placebo periods. Moreover, decreased cortical thickness was correlated with worse cognitive performance after both periods (rs=-0.54 to -0.40, not surviving FDR correction). These findings provide evidence that a four-week high phenylalanine exposure in adults with phenylketonuria results in transient reductions of the cortical grey matter and increases in white matter volume. Further research is needed to determine the potential long-term impact of high phenylalanine levels on brain structure and function in adults with phenylketonuria.

Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA-Epilepsy study.

OBJECTIVE: The intricate neuroanatomical structure of the cerebellum is of longstanding interest in epilepsy, but has been poorly characterized within the current corticocentric models of this disease. We quantified cross-sectional regional cerebellar lobule volumes using structural magnetic resonance imaging in 1602 adults with epilepsy and 1022 healthy controls across 22 sites from the global ENIGMA-Epilepsy working group. METHODS: A state-of-the-art deep learning-based approach was employed that parcellates the cerebellum into 28 neuroanatomical subregions. Linear mixed models compared total and regional cerebellar volume in (1) all epilepsies, (2) temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), (3) nonlesional temporal lobe epilepsy, (4) genetic generalized epilepsy, and (5) extratemporal focal epilepsy (ETLE). Relationships were examined for cerebellar volume versus age at seizure onset, duration of epilepsy, phenytoin treatment, and cerebral cortical thickness. RESULTS: Across all epilepsies, reduced total cerebellar volume was observed (d = .42). Maximum volume loss was observed in the corpus medullare (dmax = .49) and posterior lobe gray matter regions, including bilateral lobules VIIB (dmax = .47), crus I/II (dmax = .39), VIIIA (dmax = .45), and VIIIB (dmax = .40). Earlier age at seizure onset ( η ρ max 2 = .05) and longer epilepsy duration ( η ρ max 2 = .06) correlated with reduced volume in these regions. Findings were most pronounced in TLE-HS and ETLE, with distinct neuroanatomical profiles observed in the posterior lobe. Phenytoin treatment was associated with reduced posterior lobe volume. Cerebellum volume correlated with cerebral cortical thinning more strongly in the epilepsy cohort than in controls. SIGNIFICANCE: We provide robust evidence of deep cerebellar and posterior lobe subregional gray matter volume loss in patients with chronic epilepsy. Volume loss was maximal for posterior subregions implicated in nonmotor functions, relative to motor regions of both the anterior and posterior lobe. Associations between cerebral and cerebellar changes, and variability of neuroanatomical profiles across epilepsy syndromes argue for more precise incorporation of cerebellar subregional damage into neurobiological models of epilepsy.

Growing importance of brain morphometry analysis in the clinical routine: The hidden impact of MR sequence parameters.

Volumetric assessment based on structural MRI is increasingly recognized as an auxiliary tool to visual reading, also in examinations acquired in the clinical routine. However, MRI acquisition parameters can significantly influence these measures, which must be considered when interpreting the results on an individual patient level. This Technical Note shall demonstrate the problem. Using data from a dedicated experiment, we show the influence of two crucial sequence parameters on the GM/WM contrast and their impact on the measured volumes. A simulated contrast derived from acquisition parameters TI/TR may serve as surrogate and is highly correlated (r=0.96) with the measured contrast.

Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA-Epilepsy study.

Objective: The intricate neuroanatomical structure of the cerebellum is of longstanding interest in epilepsy, but has been poorly characterized within the current cortico-centric models of this disease. We quantified cross-sectional regional cerebellar lobule volumes using structural MRI in 1,602 adults with epilepsy and 1,022 healthy controls across twenty-two sites from the global ENIGMA-Epilepsy working group. Methods: A state-of-the-art deep learning-based approach was employed that parcellates the cerebellum into 28 neuroanatomical subregions. Linear mixed models compared total and regional cerebellar volume in i) all epilepsies; ii) temporal lobe epilepsy with hippocampal sclerosis (TLE-HS); iii) non-lesional temporal lobe epilepsy (TLE-NL); iv) genetic generalised epilepsy; and (v) extra-temporal focal epilepsy (ETLE). Relationships were examined for cerebellar volume versus age at seizure onset, duration of epilepsy, phenytoin treatment, and cerebral cortical thickness. Results: Across all epilepsies, reduced total cerebellar volume was observed (d=0.42). Maximum volume loss was observed in the corpus medullare (dmax=0.49) and posterior lobe grey matter regions, including bilateral lobules VIIB (dmax= 0.47), Crus I/II (dmax= 0.39), VIIIA (dmax=0.45) and VIIIB (dmax=0.40). Earlier age at seizure onset (ηρ2max=0.05) and longer epilepsy duration (ηρ2max=0.06) correlated with reduced volume in these regions. Findings were most pronounced in TLE-HS and ETLE with distinct neuroanatomical profiles observed in the posterior lobe. Phenytoin treatment was associated with reduced posterior lobe volume. Cerebellum volume correlated with cerebral cortical thinning more strongly in the epilepsy cohort than in controls. Significance: We provide robust evidence of deep cerebellar and posterior lobe subregional grey matter volume loss in patients with chronic epilepsy. Volume loss was maximal for posterior subregions implicated in non-motor functions, relative to motor regions of both the anterior and posterior lobe. Associations between cerebral and cerebellar changes, and variability of neuroanatomical profiles across epilepsy syndromes argue for more precise incorporation of cerebellum subregions into neurobiological models of epilepsy.

Case report: Psychosis and catatonia in an adolescent patient with adipsic hypernatremia and autoantibodies against the subfornical organ.

This is the first description of a patient in which adipsic hypernatremia, a rare autoimmune encephalitis, presented in combination with complex psychiatric symptomatology, including psychosis and catatonia. Adipsic hypernatremia is characterized by autoantibodies against the thirst center of the brain. These autoantibodies cause inflammation and apoptosis in key regions of water homeostasis, leading to lack of thirst and highly increased serum sodium. To date, the symptoms of weakness, fatigue and drowsiness have been associated with adipsic hypernatremia, but no psychiatric symptomatology. Here, we showcase the first description of an adolescent patient, in which severe and complex psychiatric symptoms presented along with adipsic hypernatremia. The patient experienced delusion, hallucinations, restlessness and pronounced depression. Further, he showed ritualized, aggressive, disinhibited and sexualized behavior, as well as self-harm and psychomotor symptoms. Due to his severe condition, he was hospitalized on the emergency unit of the child and adolescent psychiatry for 8 months. Key symptoms of the presented clinical picture are: childhood-onset complex and treatment-resistant psychosis/catatonia, pronounced behavioral problems, fatigue, absent thirst perception, hypernatremia and elevated prolactin levels. This case report renders first evidence speaking for a causal link between the autoimmune adipsic hypernatremia and the psychotic disorder. Moreover, it sheds light on a new form of autoimmune psychosis.

Clinical Evaluation of a Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis.

OBJECTIVE: To evaluate the influence of quantitative reports (QReports) on the radiological assessment of hippocampal sclerosis (HS) from MRI of patients with epilepsy in a setting mimicking clinical reality. METHODS: The study included 40 patients with epilepsy, among them 20 with structural abnormalities in the mesial temporal lobe (13 with HS). Six raters blinded to the diagnosis assessed the 3T MRI in two rounds, first using MRI only and later with both MRI and the QReport. Results were evaluated using inter-rater agreement (Fleiss' kappa [Formula: see text]) and comparison with a consensus of two radiological experts derived from clinical and imaging data, including 7T MRI. RESULTS: For the primary outcome, diagnosis of HS, the mean accuracy of the raters improved from 77.5% with MRI only to 86.3% with the additional QReport (effect size [Formula: see text]). Inter-rater agreement increased from [Formula: see text] to [Formula: see text]. Five of the six raters reached higher accuracies, and all reported higher confidence when using the QReports. CONCLUSION: In this pre-use clinical evaluation study, we demonstrated clinical feasibility and usefulness as well as the potential impact of a previously suggested imaging biomarker for radiological assessment of HS.

Large-scale transient peri-ictal perfusion magnetic resonance imaging abnormalities detected by quantitative image analysis.

Epileptic seizures require a rapid and safe diagnosis to minimize the time from onset to adequate treatment. Some epileptic seizures can be diagnosed clinically with the respective expertise. For more subtle seizures, imaging is mandatory to rule out treatable structural lesions and potentially life-threatening conditions. MRI perfusion abnormalities associated with epileptic seizures have been reported in CT and MRI studies. However, the interpretation of transient peri-ictal MRI abnormalities is routinely based on qualitative visual analysis and therefore reader dependent. In this retrospective study, we investigated the diagnostic yield of visual analysis of perfusion MRI during ictal and postictal states based on comparative expert ratings in 51 patients. We further propose an automated semi-quantitative method for perfusion analysis to determine perfusion abnormalities observed during ictal and postictal MRI using dynamic susceptibility contrast MRI, which we validated on a subcohort of 27 patients. The semi-quantitative method provides a parcellation of 3D T1-weighted images into 32 standardized cortical regions of interests and subcortical grey matter structures based on a recently proposed method, direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation for brain anatomy segmentation. Standard perfusion maps from a Food and Drug Administration-approved image analysis tool (Olea Sphere 3.0) were co-registered and investigated for region-wise differences between ictal and postictal states. These results were compared against the visual analysis of two readers experienced in functional image analysis in epilepsy. In the ictal group, cortical hyperperfusion was present in 17/18 patients (94% sensitivity), whereas in the postictal cohort, cortical hypoperfusion was present only in 9/33 (27%) patients while 24/33 (73%) showed normal perfusion. The (semi-)quantitative dynamic susceptibility contrast MRI perfusion analysis indicated increased thalamic perfusion in the ictal cohort and hypoperfusion in the postictal cohort. Visual ratings between expert readers performed well on the patient level, but visual rating agreement was low for analysis of subregions of the brain. The asymmetry of the automated image analysis correlated significantly with the visual consensus ratings of both readers. We conclude that expert analysis of dynamic susceptibility contrast MRI effectively discriminates ictal versus postictal perfusion patterns. Automated perfusion evaluation revealed favourable interpretability and correlated well with the classification of the visual ratings. It may therefore be employed for high-throughput, large-scale perfusion analysis in extended cohorts, especially for research questions with limited expert rater capacity.

Anti-neurochondrin antibody as a biomarker in primary autoimmune cerebellar ataxia-a case report and review of the literature.

BACKGROUND AND PURPOSE: Neuronal autoantibodies can support the diagnosis of primary autoimmune cerebellar ataxia (PACA). Knowledge of PACA is still sparce. This article aims to highlight the relevance of anti-neurochondrin antibodies and possible therapeutical consequences in people with PACA. METHODS: This is a case presentation and literature review of PACA associated with anti-neurochondrin antibodies. RESULTS: A 33-year-old man noticed reduced control of the right leg in May 2020. During his first clinic appointment at our institution in September 2021, he complained about gait imbalance, fine motor disorders, tremor, intermittent diplopia and slurred speech. He presented a pancerebellar syndrome with stance, gait and limb ataxia, scanning speech and oculomotor dysfunction. Within 3 months the symptoms progressed. An initial cerebral magnetic resonance imaging, June 2020, was normal, but follow-up imaging in October 2021 and July 2022 revealed marked cerebellar atrophy (29% volume loss). Cerebrospinal fluid analysis showed lymphocytic pleocytosis of 11 x 103 /L (normal range 0-4) and oligoclonal bands type II. Anti-neurochondrin antibodies (immunoglobulin G) were detected in serum (1:10,000) and cerebrospinal fluid (1:320, by cell-based indirect immunofluorescence assay and immunoblot, analysed by the EUROIMMUN laboratory). After ruling out alternative causes and neoplasia, diagnosis of PACA was given and immunotherapy (steroids and cyclophosphamide) was started in January 2022. In March 2022 a stabilization of disease was observed. CONCLUSION: Cerebellar ataxia associated with anti-neurochondrin antibodies has only been described in 19 cases; however, the number of unrecognized PACAs may be higher. As anti-neurochondrin antibodies target an intracellular antigen and exhibit a mainly cytotoxic T-cell-mediated pathogenesis, important therapeutic implications may result. Because of the severe and rapid clinical progression, aggressive immunotherapy was warranted. This case highlights the need for rapid diagnosis and therapy in PACA, as stabilization and even improvement of symptoms are attainable.

Multiple sclerosis as a model to investigate SARS-CoV-2 effect on brain atrophy.

INTRODUCTION: Data on structural brain changes after infection with SARS-CoV-2 is sparse. We postulate multiple sclerosis as a model to study the effects of SARS-CoV-2 on brain atrophy due to the unique availability of longitudinal imaging data in this patient group, enabling assessment of intraindividual brain atrophy rates. METHODS: Global and regional cortical gray matter volumes were derived from structural MRIs using FreeSurfer. A linear model was fitted to the measures of the matching pre-SARS-CoV-2 images with age as an explanatory variable. The residuals were used to determine whether the post-SARS-CoV-2 volumes differed significantly from the baseline. RESULTS: Fourteen RRMS patients with a total of 113 longitudinal magnetic resonance images were retrospectively analyzed. We found no acceleration of brain atrophy after infection with SARS-CoV-2 for global gray matter volume (p = 0.17). However, on the regional level, parahippocampal gyri showed a tendency toward volume reduction (p = 0.0076), suggesting accelerated atrophy during or after infection. CONCLUSIONS: Our results illustrate the opportunity of using longitudinal MRIs from existing MS registries to study brain changes associated with SARS-CoV-2 infections. We would like to address the global MS community with a call for action to use the available cohorts, reproduce the proposed analysis, and pool the results.

Reliable brain morphometry from contrast-enhanced T1w-MRI in patients with multiple sclerosis.

Brain morphometry is usually based on non-enhanced (pre-contrast) T1-weighted MRI. However, such dedicated protocols are sometimes missing in clinical examinations. Instead, an image with a contrast agent is often available. Existing tools such as FreeSurfer yield unreliable results when applied to contrast-enhanced (CE) images. Consequently, these acquisitions are excluded from retrospective morphometry studies, which reduces the sample size. We hypothesize that deep learning (DL)-based morphometry methods can extract morphometric measures also from contrast-enhanced MRI. We have extended DL+DiReCT to cope with contrast-enhanced MRI. Training data for our DL-based model were enriched with non-enhanced and CE image pairs from the same session. The segmentations were derived with FreeSurfer from the non-enhanced image and used as ground truth for the coregistered CE image. A longitudinal dataset of patients with multiple sclerosis (MS), comprising relapsing remitting (RRMS) and primary progressive (PPMS) subgroups, was used for the evaluation. Global and regional cortical thickness derived from non-enhanced and CE images were contrasted to results from FreeSurfer. Correlation coefficients of global mean cortical thickness between non-enhanced and CE images were significantly larger with DL+DiReCT (r = 0.92) than with FreeSurfer (r = 0.75). When comparing the longitudinal atrophy rates between the two MS subgroups, the effect sizes between PPMS and RRMS were higher with DL+DiReCT both for non-enhanced (d = -0.304) and CE images (d = -0.169) than for FreeSurfer (non-enhanced d = -0.111, CE d = 0.085). In conclusion, brain morphometry can be derived reliably from contrast-enhanced MRI using DL-based morphometry tools, making additional cases available for analysis and potential future diagnostic morphometry tools.

Hippocampal volume in patients with bilateral and unilateral peripheral vestibular dysfunction.

Previous studies have found that peripheral vestibular dysfunction is associated with altered volumes in different brain structures, especially in the hippocampus. However, published evidence is conflicting. Based on previous findings, we compared hippocampal volume, as well as supramarginal, superior temporal, and postcentral gyrus in a sample of 55 patients with different conditions of peripheral vestibular dysfunction (bilateral, chronic unilateral, acute unilateral) to 39 age- and sex-matched healthy controls. In addition, we explored deviations in gray-matter volumes in hippocampal subfields. We also analysed correlations between morphometric data and visuo-spatial performance. Patients with vestibular dysfunction did not differ in total hippocampal volume from healthy controls. However, a reduced volume in the right presubiculum of the hippocampus and the left supramarginal gyrus was observed in patients with chronic and acute unilateral vestibular dysfunction, but not in patients with bilateral vestibular dysfunction. No association of altered volumes with visuo-spatial performance was found. An asymmetric vestibular input due to unilateral vestibular dysfunction might lead to reduced central brain volumes that are involved in vestibular processing.

Cortical thickness and its relationship to cognitive performance and metabolic control in adults with phenylketonuria.

Despite good control of phenylalanine (Phe) levels during childhood and adolescence, adults with phenylketonuria (PKU) often show abnormalities in the white matter of the brain, which have been associated with poorer cognitive performance. However, whether such a relationship exists with cortical gray matter is still unknown. Therefore, we investigated cortical thickness and surface area in adults with early-treated PKU and their relationship to cognitive functions and metabolic control. We included 30 adult patients with early-treated and metabolically well-controlled PKU (median age: 35.5 years) and 54 healthy controls (median age: 29.3 years). Surface-based morphometry was derived from T1-weighted magnetic resonance images using FreeSurfer, and general intelligence, executive functions, and attention were assessed. Concurrent plasma Phe, tyrosine, and tryptophan levels were measured in patients. In addition, Phe levels were collected retrospectively to calculate the index of dietary control. Patients showed a thinner cortex than controls in regions of the bilateral temporal, parietal, and occipital lobes (effect size r = -0.34 to -0.42, p < 0.05). No group differences in surface area were found. In patients, accuracy in the working memory task was positively correlated with thickness in the left insula (r = 0.45, p = 0.013), left fusiform gyrus (r = 0.39, p = 0.032), and right superior temporal gyrus (r = 0.41, p = 0.024), but did not survive false discovery rate correction. Neither concurrent nor historical metabolic parameters were related to cortical thickness. Taken together, adults with PKU showed widespread reductions in cortical thickness despite good metabolic control in childhood and adolescence. However, alterations in cortical thickness were unrelated to metabolic parameters and cognitive performance.

A Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI.

PURPOSE: Hippocampal volumetry is an important biomarker to quantify atrophy in patients with mesial temporal lobe epilepsy. We investigate the sensitivity of automated segmentation methods to support radiological assessments of hippocampal sclerosis (HS). Results from FreeSurfer and FSL-FIRST are contrasted to a deep learning (DL)-based segmentation method. MATERIALS AND METHODS: We used T1-weighted MRI scans from 105 patients with epilepsy and 354 healthy controls. FreeSurfer, FSL, and a DL-based method were applied for brain anatomy segmentation. We calculated effect sizes (Cohen's d) between left/right HS and healthy controls based on the asymmetry of hippocampal volumes. Additionally, we derived 14 shape features from the segmentations and determined the most discriminating feature to identify patients with hippocampal sclerosis by a support vector machine (SVM). RESULTS: Deep learning-based segmentation of the hippocampus was the most sensitive to detecting HS. The effect sizes of the volume asymmetries were larger with the DL-based segmentations (HS left d= -4.2, right = 4.2) than with FreeSurfer (left= -3.1, right = 3.7) and FSL (left= -2.3, right = 2.5). For the classification based on the shape features, the surface-to-volume ratio was identified as the most important feature. Its absolute asymmetry yielded a higher area under the curve (AUC) for the deep learning-based segmentation (AUC = 0.87) than for FreeSurfer (0.85) and FSL (0.78) to dichotomize HS from other epilepsy cases. The robustness estimated from repeated scans was statistically significantly higher with DL than all other methods. CONCLUSION: Our findings suggest that deep learning-based segmentation methods yield a higher sensitivity to quantify hippocampal sclerosis than atlas-based methods and derived shape features are more robust. We propose an increased asymmetry in the surface-to-volume ratio of the hippocampus as an easy-to-interpret quantitative imaging biomarker for HS.

Topographic divergence of atypical cortical asymmetry and atrophy patterns in temporal lobe epilepsy.

Temporal lobe epilepsy, a common drug-resistant epilepsy in adults, is primarily a limbic network disorder associated with predominant unilateral hippocampal pathology. Structural MRI has provided an in vivo window into whole-brain grey matter structural alterations in temporal lobe epilepsy relative to controls, by either mapping (i) atypical inter-hemispheric asymmetry; or (ii) regional atrophy. However, similarities and differences of both atypical asymmetry and regional atrophy measures have not been systematically investigated. Here, we addressed this gap using the multisite ENIGMA-Epilepsy dataset comprising MRI brain morphological measures in 732 temporal lobe epilepsy patients and 1418 healthy controls. We compared spatial distributions of grey matter asymmetry and atrophy in temporal lobe epilepsy, contextualized their topographies relative to spatial gradients in cortical microstructure and functional connectivity calculated using 207 healthy controls obtained from Human Connectome Project and an independent dataset containing 23 temporal lobe epilepsy patients and 53 healthy controls and examined clinical associations using machine learning. We identified a marked divergence in the spatial distribution of atypical inter-hemispheric asymmetry and regional atrophy mapping. The former revealed a temporo-limbic disease signature while the latter showed diffuse and bilateral patterns. Our findings were robust across individual sites and patients. Cortical atrophy was significantly correlated with disease duration and age at seizure onset, while degrees of asymmetry did not show a significant relationship to these clinical variables. Our findings highlight that the mapping of atypical inter-hemispheric asymmetry and regional atrophy tap into two complementary aspects of temporal lobe epilepsy-related pathology, with the former revealing primary substrates in ipsilateral limbic circuits and the latter capturing bilateral disease effects. These findings refine our notion of the neuropathology of temporal lobe epilepsy and may inform future discovery and validation of complementary MRI biomarkers in temporal lobe epilepsy.

QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results.

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraTS.

Somatotopy of cervical dystonia in motor-cerebellar networks: Evidence from resting state fMRI.

INTRODUCTION: Cervical dystonia is the most frequent form of isolated focal dystonia. It is often associated with a dysfunction in brain networks, mostly affecting the basal ganglia, the cerebellum, and the somatosensory cortex. However, it is unclear if such a dysfunction is somato-specific to the brain areas containing the representation of the affected body part, and may thereby account for the focal expression of cervical dystonia. In this study, we investigated resting state functional connectivity in the areas within the motor cortex and the cerebellum containing affected and non-affected body representations in cervical dystonia patients. METHODS: Eighteen patients affected by cervical dystonia and 21 healthy controls had resting state fMRI. The functional connectivity between the motor cortex and the cerebellum, as well as their corresponding measures of gray matter volume and cortical thickness, were compared between groups. We performed seed-based analyses, selecting the different body representation areas in the precentral gyrus as seed regions, and all cerebellar areas as target regions. RESULTS: Compared to controls, patients exhibited increased functional connectivity between the bilateral trunk representation area of the motor cortex and the cerebellar vermis 6 and 7b, respectively. These functional abnormalities did not correlate with structural changes or symptom severity. CONCLUSIONS: Our findings indicate that the abnormal function of the motor network is somato-specific to the areas encompassing the neck representation. Functional abnormalities in discrete relevant areas of the motor network could thus contribute to the focal expression of CD.

Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation.

Accurate and reliable measures of cortical thickness from magnetic resonance imaging are an important biomarker to study neurodegenerative and neurological disorders. Diffeomorphic registration-based cortical thickness (DiReCT) is a known technique to derive such measures from non-surface-based volumetric tissue maps. ANTs provides an open-source method for estimating cortical thickness, derived by applying DiReCT to an atlas-based segmentation. In this paper, we propose DL+DiReCT, a method using high-quality deep learning-based neuroanatomy segmentations followed by DiReCT, yielding accurate and reliable cortical thickness measures in a short time. We evaluate the methods on two independent datasets and compare the results against surface-based measures from FreeSurfer. Good correlation of DL+DiReCT with FreeSurfer was observed (r = .887) for global mean cortical thickness compared to ANTs versus FreeSurfer (r = .608). Experiments suggest that both DiReCT-based methods had higher sensitivity to changes in cortical thickness than Freesurfer. However, while ANTs showed low scan-rescan robustness, DL+DiReCT showed similar robustness to Freesurfer. Effect-sizes for group-wise differences of healthy controls compared to individuals with dementia were highest with the deep learning-based segmentation. DL+DiReCT is a promising combination of a deep learning-based method with a traditional registration technique to detect subtle changes in cortical thickness.

The ENIGMA-Epilepsy working group: Mapping disease from large data sets.

Epilepsy is a common and serious neurological disorder, with many different constituent conditions characterized by their electro clinical, imaging, and genetic features. MRI has been fundamental in advancing our understanding of brain processes in the epilepsies. Smaller-scale studies have identified many interesting imaging phenomena, with implications both for understanding pathophysiology and improving clinical care. Through the infrastructure and concepts now well-established by the ENIGMA Consortium, ENIGMA-Epilepsy was established to strengthen epilepsy neuroscience by greatly increasing sample sizes, leveraging ideas and methods established in other ENIGMA projects, and generating a body of collaborating scientists and clinicians to drive forward robust research. Here we review published, current, and future projects, that include structural MRI, diffusion tensor imaging (DTI), and resting state functional MRI (rsfMRI), and that employ advanced methods including structural covariance, and event-based modeling analysis. We explore age of onset- and duration-related features, as well as phenomena-specific work focusing on particular epilepsy syndromes or phenotypes, multimodal analyses focused on understanding the biology of disease progression, and deep learning approaches. We encourage groups who may be interested in participating to make contact to further grow and develop ENIGMA-Epilepsy.

Brain Morphometry Estimation: From Hours to Seconds Using Deep Learning.

Motivation: Brain morphometry from magnetic resonance imaging (MRI) is a promising neuroimaging biomarker for the non-invasive diagnosis and monitoring of neurodegenerative and neurological disorders. Current tools for brain morphometry often come with a high computational burden, making them hard to use in clinical routine, where time is often an issue. We propose a deep learning-based approach to predict the volumes of anatomically delineated subcortical regions of interest (ROI), and mean thicknesses and curvatures of cortical parcellations directly from T1-weighted MRI. Advantages are the timely availability of results while maintaining a clinically relevant accuracy. Materials and Methods: An anonymized dataset of 574 subjects (443 healthy controls and 131 patients with epilepsy) was used for the supervised training of a convolutional neural network (CNN). A silver-standard ground truth was generated with FreeSurfer 6.0. Results: The CNN predicts a total of 165 morphometric measures directly from raw MR images. Analysis of the results using intraclass correlation coefficients showed, in general, good correlation with FreeSurfer generated ground truth data, with some of the regions nearly reaching human inter-rater performance (ICC > 0.75). Cortical thicknesses predicted by the CNN showed cross-sectional annual age-related gray matter atrophy rates both globally (thickness change of -0.004 mm/year) and regionally in agreement with the literature. A statistical test to dichotomize patients with epilepsy from healthy controls revealed similar effect sizes for structures affecting all subtypes as reported in a large-scale epilepsy study. Conclusions: We demonstrate the general feasibility of using deep learning to estimate human brain morphometry directly from T1-weighted MRI within seconds. A comparison of the results to other publications shows accuracies of comparable magnitudes for the subcortical volumes and cortical thicknesses.