Development of Gestational Age-Based Fetal Brain and Intracranial Volume Reference Norms Using Deep Learning.

BACKGROUND AND PURPOSE: Fetal brain MR imaging interpretations are subjective and require subspecialty expertise. We aimed to develop a deep learning algorithm for automatically measuring intracranial and brain volumes of fetal brain MRIs across gestational ages. MATERIALS AND METHODS: This retrospective study included 246 patients with singleton pregnancies at 19-38 weeks gestation. A 3D U-Net was trained to segment the intracranial contents of 2D fetal brain MRIs in the axial, coronal, and sagittal planes. An additional 3D U-Net was trained to segment the brain from the output of the first model. Models were tested on MRIs of 10 patients (28 planes) via Dice coefficients and volume comparison with manual reference segmentations. Trained U-Nets were applied to 200 additional MRIs to develop normative reference intracranial and brain volumes across gestational ages and then to 9 pathologic fetal brains. RESULTS: Fetal intracranial and brain compartments were automatically segmented in a mean of 6.8 (SD, 1.2) seconds with median Dices score of 0.95 and 0.90, respectively (interquartile ranges, 0.91-0.96/0.89-0.91) on the test set. Correlation with manual volume measurements was high (Pearson r = 0.996, P < .001). Normative samples of intracranial and brain volumes across gestational ages were developed. Eight of 9 pathologic fetal intracranial volumes were automatically predicted to be >2 SDs from this age-specific reference mean. There were no effects of fetal sex, maternal diabetes, or maternal age on intracranial or brain volumes across gestational ages. CONCLUSIONS: Deep learning techniques can quickly and accurately quantify intracranial and brain volumes on clinical fetal brain MRIs and identify abnormal volumes on the basis of a normative reference standard.

Convolutional Neural Network for Automated FLAIR Lesion Segmentation on Clinical Brain MR Imaging.

BACKGROUND AND PURPOSE: Most brain lesions are characterized by hyperintense signal on FLAIR. We sought to develop an automated deep learning-based method for segmentation of abnormalities on FLAIR and volumetric quantification on clinical brain MRIs across many pathologic entities and scanning parameters. We evaluated the performance of the algorithm compared with manual segmentation and existing automated methods. MATERIALS AND METHODS: We adapted a U-Net convolutional neural network architecture for brain MRIs using 3D volumes. This network was retrospectively trained on 295 brain MRIs to perform automated FLAIR lesion segmentation. Performance was evaluated on 92 validation cases using Dice scores and voxelwise sensitivity and specificity, compared with radiologists' manual segmentations. The algorithm was also evaluated on measuring total lesion volume. RESULTS: Our model demonstrated accurate FLAIR lesion segmentation performance (median Dice score, 0.79) on the validation dataset across a large range of lesion characteristics. Across 19 neurologic diseases, performance was significantly higher than existing methods (Dice, 0.56 and 0.41) and approached human performance (Dice, 0.81). There was a strong correlation between the predictions of lesion volume of the algorithm compared with true lesion volume (ρ = 0.99). Lesion segmentations were accurate across a large range of image-acquisition parameters on >30 different MR imaging scanners. CONCLUSIONS: A 3D convolutional neural network adapted from a U-Net architecture can achieve high automated FLAIR segmentation performance on clinical brain MR imaging across a variety of underlying pathologies and image acquisition parameters. The method provides accurate volumetric lesion data that can be incorporated into assessments of disease burden or into radiologic reports.

The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism.

Autism spectrum disorders (ASDs) represent a formidable challenge for psychiatry and neuroscience because of their high prevalence, lifelong nature, complexity and substantial heterogeneity. Facing these obstacles requires large-scale multidisciplinary efforts. Although the field of genetics has pioneered data sharing for these reasons, neuroimaging had not kept pace. In response, we introduce the Autism Brain Imaging Data Exchange (ABIDE)-a grassroots consortium aggregating and openly sharing 1112 existing resting-state functional magnetic resonance imaging (R-fMRI) data sets with corresponding structural MRI and phenotypic information from 539 individuals with ASDs and 573 age-matched typical controls (TCs; 7-64 years) (http://fcon_1000.projects.nitrc.org/indi/abide/). Here, we present this resource and demonstrate its suitability for advancing knowledge of ASD neurobiology based on analyses of 360 male subjects with ASDs and 403 male age-matched TCs. We focused on whole-brain intrinsic functional connectivity and also survey a range of voxel-wise measures of intrinsic functional brain architecture. Whole-brain analyses reconciled seemingly disparate themes of both hypo- and hyperconnectivity in the ASD literature; both were detected, although hypoconnectivity dominated, particularly for corticocortical and interhemispheric functional connectivity. Exploratory analyses using an array of regional metrics of intrinsic brain function converged on common loci of dysfunction in ASDs (mid- and posterior insula and posterior cingulate cortex), and highlighted less commonly explored regions such as the thalamus. The survey of the ABIDE R-fMRI data sets provides unprecedented demonstrations of both replication and novel discovery. By pooling multiple international data sets, ABIDE is expected to accelerate the pace of discovery setting the stage for the next generation of ASD studies.

Altered functional and structural brain network organization in autism.

Structural and functional underconnectivity have been reported for multiple brain regions, functional systems, and white matter tracts in individuals with autism spectrum disorders (ASD). Although recent developments in complex network analysis have established that the brain is a modular network exhibiting small-world properties, network level organization has not been carefully examined in ASD. Here we used resting-state functional MRI (n = 42 ASD, n = 37 typically developing; TD) to show that children and adolescents with ASD display reduced short and long-range connectivity within functional systems (i.e., reduced functional integration) and stronger connectivity between functional systems (i.e., reduced functional segregation), particularly in default and higher-order visual regions. Using graph theoretical methods, we show that pairwise group differences in functional connectivity are reflected in network level reductions in modularity and clustering (local efficiency), but shorter characteristic path lengths (higher global efficiency). Structural networks, generated from diffusion tensor MRI derived fiber tracts (n = 51 ASD, n = 43 TD), displayed lower levels of white matter integrity yet higher numbers of fibers. TD and ASD individuals exhibited similar levels of correlation between raw measures of structural and functional connectivity (n = 35 ASD, n = 35 TD). However, a principal component analysis combining structural and functional network properties revealed that the balance of local and global efficiency between structural and functional networks was reduced in ASD, positively correlated with age, and inversely correlated with ASD symptom severity. Overall, our findings suggest that modeling the brain as a complex network will be highly informative in unraveling the biological basis of ASD and other neuropsychiatric disorders.