Interpreting Age Effects of Human Fetal Brain from Spontaneous fMRI using Deep 3D Convolutional Neural Networks

Understanding human fetal neurodevelopment is of great clinical importance as abnormal development is linked to adverse neuropsychiatric outcomes after birth. Recent advances in functional Magnetic Resonance Imaging (fMRI) have provided new insight into development of the human brain before birth, but these studies have predominately focused on brain functional connectivity (i.e. Fisher z-score), which requires manual processing steps for feature extraction from fMRI images. Deep learning approaches (i.e., Convolutional Neural Networks) have achieved remarkable success on learning directly from image data, yet have not been applied on fetal fMRI for understanding fetal neurodevelopment. Here, we bridge this gap by applying a novel application of deep 3D CNN to fetal blood oxygen-level dependence (BOLD) resting-state fMRI data. Specifically, we test a supervised CNN framework as a data-driven approach to isolate variation in fMRI signals that relate to younger v.s. older fetal age groups. Based on the learned CNN, we further perform sensitivity analysis to identify brain regions in which changes in BOLD signal are strongly associated with fetal brain age. The findings demonstrate that deep CNNs are a promising approach for identifying spontaneous functional patterns in fetal brain activity that discriminate age groups. Further, we discovered that regions that most strongly differentiate groups are largely bilateral, share similar distribution in older and younger age groups, and are areas of heightened metabolic activity in early human development.Comment: 9 page

Single-Input Multi-Output U-Net for Automated 2D Foetal Brain Segmentation of MR Images

In this work, we develop the Single-Input Multi-Output U-Net (SIMOU-Net), a hybrid network for foetal brain segmentation inspired by the original U-Net fused with the holistically nested edge detection (HED) network. The SIMOU-Net is similar to the original U-Net but it has a deeper architecture and takes account of the features extracted from each side output. It acts similar to an ensemble neural network, however, instead of averaging the outputs from several independently trained models, which is computationally expensive, our approach combines outputs from a single network to reduce the variance of predications and generalization errors. Experimental results using 200 normal foetal brains consisting of over 11,500 2D images produced Dice and Jaccard coefficients of 94.2 ± 5.9% and 88.7 ± 6.9%, respectively. We further tested the proposed network on 54 abnormal cases (over 3500 images) and achieved Dice and Jaccard coefficients of 91.2 ± 6.8% and 85.7 ± 6.6%, respectively

Approche hiérarchique pour la segmentation du cervelet en IRM chez le nouveau-né : une étude expérimentale

International audienceMorphometric analysis of brain structures is of high interest for premature neonates, in particular for defining predictive neurodevelopment biomarkers. This requires beforehand, the correct segmentation of structures of interest from MR images. Such segmentation is however complex, due to the resolution and properties of data. In this context, we investigate the potential of hierarchical image models, and more precisely the binary partition tree, as a way of developing efficient, interactive and user-friendly 3D segmentation methods. In particular, we experiment the relevance of texture features for defining the hierarchy of partittions constituting the final segmentation space. This is one of the first uses of binary partition trees for 3D segmentation of medical images. Experiments are carried out on 19 MR images for cerebellum segmentation purpose.L'analyse morphométrique des structures cérébrales chez le prématuré est un sujet de plus en plus étu-dié dans le milieu médical afin de définir des biomar-queurs de neurodéveloppement. Cela nécessite dans un premier temps une segmentation de bonne qualité des structures d'intérêt à partir d'IRM cérébrales. Ce type de segmentation est complexe à réaliser en raison de la résolution et des propriétés des IRM. Dans ce contexte, nous étudions le potentiel des modèles hiérarchiques et plus précisément l'arbre binaire de partitions, comme outil de segmentation 3D interactive et d'utilisation aisée. En particulier, nous étudions l'intérêt des textures pour définir la structure hiérarchique fournissant la segmentation finale. Ce travail constitue l'une des premières utilisations des arbres binaires de partitions pour la segmentation 3D d'images médicales. Les ex-périences sont réalisées sur 19 images IRM pour la segmentation du cervelet

A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

Background: Spina bifida aperta (SBA) is a birth defect associated with severe anatomical changes in the developing fetal brain. Brain magnetic resonance imaging (MRI) atlases are popular tools for studying neuropathology in the brain anatomy, but previous fetal brain MRI atlases have focused on the normal fetal brain. We aimed to develop a spatio-temporal fetal brain MRI atlas for SBA. Methods: We developed a semi-automatic computational method to compute the first spatio-temporal fetal brain MRI atlas for SBA. We used 90 MRIs of fetuses with SBA with gestational ages ranging from 21 to 35 weeks. Isotropic and motion-free 3D reconstructed MRIs were obtained for all the examinations. We propose a protocol for the annotation of anatomical landmarks in brain 3D MRI of fetuses with SBA with the aim of making spatial alignment of abnormal fetal brain MRIs more robust. In addition, we propose a weighted generalized Procrustes method based on the anatomical landmarks for the initialization of the atlas. The proposed weighted generalized Procrustes can handle temporal regularization and missing annotations. After initialization, the atlas is refined iteratively using non-linear image registration based on the image intensity and the anatomical land-marks. A semi-automatic method is used to obtain a parcellation of our fetal brain atlas into eight tissue types: white matter, ventricular system, cerebellum, extra-axial cerebrospinal fluid, cortical gray matter, deep gray matter, brainstem, and corpus callosum. Results: An intra-rater variability analysis suggests that the seven anatomical land-marks are sufficiently reliable. We find that the proposed atlas outperforms a normal fetal brain atlas for the automatic segmentation of brain 3D MRI of fetuses with SBA. Conclusions: We make publicly available a spatio-temporal fetal brain MRI atlas for SBA, available here: https://doi.org/10.7303/syn25887675. This atlas can support future research on automatic segmentation methods for brain 3D MRI of fetuses with SBA

A spatio-temporal atlas of the developing fetal brain with spina bifida aperta

Background: Spina bifida aperta (SBA) is a birth defect associated with severe anatomical changes in the developing fetal brain. Brain magnetic resonance imaging (MRI) atlases are popular tools for studying neuropathology in the brain anatomy, but previous fetal brain MRI atlases have focused on the normal fetal brain. We aimed to develop a spatio-temporal fetal brain MRI atlas for SBA. Methods: We developed a semi-automatic computational method to compute the first spatio-temporal fetal brain MRI atlas for SBA. We used 90 MRIs of fetuses with SBA with gestational ages ranging from 21 to 35 weeks. Isotropic and motion-free 3D reconstructed MRIs were obtained for all the examinations. We propose a protocol for the annotation of anatomical landmarks in brain 3D MRI of fetuses with SBA with the aim of making spatial alignment of abnormal fetal brain MRIs more robust. In addition, we propose a weighted generalized Procrustes method based on the anatomical landmarks for the initialization of the atlas. The proposed weighted generalized Procrustes can handle temporal regularization and missing annotations. After initialization, the atlas is refined iteratively using non-linear image registration based on the image intensity and the anatomical land-marks. A semi-automatic method is used to obtain a parcellation of our fetal brain atlas into eight tissue types: white matter, ventricular system, cerebellum, extra-axial cerebrospinal fluid, cortical gray matter, deep gray matter, brainstem, and corpus callosum. Results: An intra-rater variability analysis suggests that the seven anatomical land-marks are sufficiently reliable. We find that the proposed atlas outperforms a normal fetal brain atlas for the automatic segmentation of brain 3D MRI of fetuses with SBA. Conclusions: We make publicly available a spatio-temporal fetal brain MRI atlas for SBA, available here: https://doi.org/10.7303/syn25887675. This atlas can support future research on automatic segmentation methods for brain 3D MRI of fetuses with SBA

Maternal Interleukin-6 concentration during pregnancy is associated with variation in frontolimbic white matter and cognitive development in early life

Maternal inflammation during pregnancy can alter the trajectory of fetal brain development and increase risk for offspring psychiatric disorders. However, the majority of relevant research to date has been conducted in animal models. Here, in humans, we focus on the structural connectivity of frontolimbic circuitry as it is both critical for socioemotional and cognitive development, and commonly altered in a range of psychiatric disorders associated with intrauterine inflammation. Specifically, we test the hypothesis that elevated maternal concentration of the proinflammatory cytokine interleukin-6 (IL-6) during pregnancy will be associated with variation in microstructural properties of this circuitry in the neonatal period and across the first year of life. Pregnant mothers were recruited in early pregnancy and maternal blood samples were obtained for assessment of maternal IL-6 concentrations in early (12.6 ± 2.8 weeks [S.D.]), mid (20.4 ± 1.5 weeks [S.D.]) and late (30.3 ± 1.3 weeks [S.D.]) gestation. Offspring brain MRI scans were acquired shortly after birth (N = 86, scan age = 3.7 ± 1.7 weeks [S.D.]) and again at 12-mo age (N = 32, scan age = 54.0 ± 3.1 weeks [S.D.]). Diffusion Tensor Imaging (DTI) was used to characterize fractional anisotropy (FA) along the left and right uncinate fasciculus (UF), representing the main frontolimbic fiber tract. In N = 30 of the infants with serial MRI data at birth and 12-mo age, cognitive and socioemotional developmental status was characterized using the Bayley Scales of Infant Development. All analyses tested for potentially confounding influences of household income, prepregnancy Body-Mass-Index, obstetric risk, smoking during pregnancy, and infant sex, and outcomes at 12-mo age were additionally adjusted for the quality of the postnatal caregiving environment. Maternal IL-6 concentration (averaged across pregnancy) was prospectively and inversely associated with FA (suggestive of reduced integrity under high inflammatory conditions) in the newborn offspring (bi-lateral, p < 0.01) in the central portion of the UF proximal to the amygdala. Furthermore, maternal IL-6 concentration was positively associated with rate of FA increase across the first year of life (bi-lateral, p < 0.05), resulting in a null association between maternal IL-6 and UF FA at 12-mo age. Maternal IL-6 was also inversely associated with offspring cognition at 12-mo age, and this association was mediated by FA growth across the first year of postnatal life. Findings from the current study support the premise that susceptibility for cognitive impairment and potentially psychiatric disorders may be affected in utero, and that maternal inflammation may constitute an intrauterine condition of particular importance in this context

Brain segmentation in patients with perinatal arterial ischemic stroke

BACKGROUND: Perinatal arterial ischemic stroke (PAIS) is associated with adverse neurological outcomes. Quantification of ischemic lesions and consequent brain development in newborn infants relies on labor-intensive manual assessment of brain tissues and ischemic lesions. Hence, we propose an automatic method utilizing convolutional neural networks (CNNs) to segment brain tissues and ischemic lesions in MRI scans of infants suffering from PAIS. MATERIALS AND METHODS: This single-center retrospective study included 115 patients with PAIS that underwent MRI after the stroke onset (baseline) and after three months (follow-up). Nine baseline and 12 follow-up MRI scans were manually annotated to provide reference segmentations (white matter, gray matter, basal ganglia and thalami, brainstem, ventricles, extra-ventricular cerebrospinal fluid, and cerebellum, and additionally on the baseline scans the ischemic lesions). Two CNNs were trained to perform automatic segmentation on the baseline and follow-up MRIs, respectively. Automatic segmentations were quantitatively evaluated using the Dice coefficient (DC) and the mean surface distance (MSD). Volumetric agreement between segmentations that were manually and automatically obtained was computed. Moreover, the scan quality and automatic segmentations were qualitatively evaluated in a larger set of MRIs without manual annotation by two experts. In addition, the scan quality was qualitatively evaluated in these scans to establish its impact on the automatic segmentation performance. RESULTS: Automatic brain tissue segmentation led to a DC and MSD between 0.78-0.92 and 0.18-1.08 mm for baseline, and between 0.88-0.95 and 0.10-0.58 mm for follow-up scans, respectively. For the ischemic lesions at baseline the DC and MSD were between 0.72-0.86 and 1.23-2.18 mm, respectively. Volumetric measurements indicated limited oversegmentation of the extra-ventricular cerebrospinal fluid in both the follow-up and baseline scans, oversegmentation of the ischemic lesions in the left hemisphere, and undersegmentation of the ischemic lesions in the right hemisphere. In scans without imaging artifacts, brain tissue segmentation was graded as excellent in more than 85% and 91% of cases, respectively for the baseline and follow-up scans. For the ischemic lesions at baseline, this was in 61% of cases. CONCLUSIONS: Automatic segmentation of brain tissue and ischemic lesions in MRI scans of patients with PAIS is feasible. The method may allow evaluation of the brain development and efficacy of treatment in large datasets