Automatic segmentation of infant brain MR images: With special reference to myelinated white matter

Patch-based 3D U-Net and transfer learning for longitudinal piglet brain segmentation on MRI

BACKGROUND AND OBJECTIVES

In order to study neural plasticity in immature brain following early brain lesion, large animal model are needed. Because of its morphological similarities with the human developmental brain, piglet is a suitable but little used one. Its study from Magnetic Resonance Imaging (MRI) requires the development of automatic algorithms for the segmentation of the different structures and tissues. A crucial preliminary step consists in automatically segmenting the brain.

METHODS

We propose a fully automatic brain segmentation method applied to piglets by combining a 3D patch-based U-Net and a post-processing pipeline for spatial regularization and elimination of false positives. Our approach also integrates a transfer-learning strategy for managing an automated longitudinal monitoring evaluated for four developmental stages (2, 6, 10 and 18 weeks), facing the issue of MRI changes resulting from the rapid brain development. It is compared to a 2D approach and the Brain Extraction Tool (BET) as well as techniques adapted to other animals (rodents, macaques). The influence of training patches size and distribution is studied as well as the benefits of spatial regularization.

RESULTS

Results show that our approach is efficient in terms of average Dice score (0.952) and Hausdorff distance (8.51), outperforming the use of a 2D U-Net (Dice: 0.919, Hausdorff distance: 11.06) and BET (Dice: 0.764, Hausdorff distance: 25.91). The transfer-learning strategy achieves a good performance on older piglets (Dice of 0.934 at 6 weeks, 0.956 at 10 weeks and 0.958 at 18 weeks) compared to a standard training strategy with few data (Dice of 0.636 at 6 weeks, 0.907 at 10 weeks, not calculable at 18 weeks because of too few training piglets).

CONCLUSIONS

In conclusion, we provide a method for longitudinal MRI piglet brain segmentation based on 3D U-Net and transfer learning which can be used for future morphometric studies and applied to other animals.

Visual analysis of automated segmentation in the diagnosis of focal cortical dysplasias with magnetic resonance imaging

Focal cortical dysplasias (FCDs) are a frequent cause of epilepsy. It has been reported that up to 40% of them cannot be visualized with conventional magnetic resonance imaging (MRI). The main objective of this work was to evaluate by means of a retrospective descriptive observational study whether the automated brain segmentation is useful for detecting FCD. One hundred and fifty-five patients, who underwent surgery between the years 2009 and 2016, were reviewed. Twenty patients with FCD confirmed by histology and a preoperative segmentation study, with ages ranging from 3 to 43 years (14 men), were analyzed. Three expert neuroradiologists visually analyzed conventional and advanced MRI with automated segmentation. They were classified into positive and negative concerning visualization of FCD by consensus. Of the 20 patients evaluated with conventional MRI, 12 were positive for FCD. Of the negative studies for FCD with conventional MRI, 2 (25%) were positive when they were analyzed with automated segmentation. In 13 of the 20 patients (with positive segmentation for FCD), cortical thickening was observed in 5 (38.5%), while pseudothickening was observed in the rest of patients (8, 61.5%) in the anatomical region of the brain corresponding to the dysplasia. This work demonstrated that automated brain segmentation helps to increase detection of FCDs that are unable to be visualized in conventional MRI images.

A Novel Approach for Manual Segmentation of the Amygdala and Hippocampus in Neonate MRI

The gross anatomy of the infant brain at term is fairly similar to that of the adult brain, but structures are immature, and the brain undergoes rapid growth during the first 2 years of life. Neonate magnetic resonance (MR) images have different contrasts compared to adult images, and automated segmentation of brain magnetic resonance imaging (MRI) can thus be considered challenging as less software options are available. Despite this, most anatomical regions are identifiable and thus amenable to manual segmentation. In the current study, we developed a protocol for segmenting the amygdala and hippocampus in T2-weighted neonatal MR images. The participants were 31 healthy infants between 2 and 5 weeks of age. Intra-rater reliability was measured in 12 randomly selected MR images, where 6 MR images were segmented at 1-month intervals between the delineations, and another 6 MR images at 6-month intervals. The protocol was also tested by two independent raters in 20 randomly selected T2-weighted images, and finally with T1 images. Intraclass correlation coefficient (ICC) and Dice similarity coefficient (DSC) for intra-rater, inter-rater, and T1 vs. T2 comparisons were computed. Moreover, manual segmentations were compared to automated segmentations performed by iBEAT toolbox in 10 T2-weighted MR images. The intra-rater reliability was high ICC ≥ 0.91, DSC ≥ 0.89, the inter-rater reliabilities were satisfactory ICC ≥ 0.90, DSC ≥ 0.75 for hippocampus and DSC ≥ 0.52 for amygdalae. Segmentations for T1 vs. T2-weighted images showed high consistency ICC ≥ 0.90, DSC ≥ 0.74. The manual and iBEAT segmentations showed no agreement, DSC ≥ 0.39. In conclusion, there is a clear need to improve and develop the procedures for automated segmentation of infant brain MR images.

Quantitative assessment of myelination patterns in preterm neonates using T2-weighted MRI

Myelination is considered to be an important developmental process during human brain maturation and closely correlated with gestational age. Quantitative assessment of the myelination status requires dedicated imaging, but the conventional T₂-weighted scans routinely acquired during clinical imaging of neonates carry signatures that are thought to be associated with myelination. In this work, we develop a quatitative marker of progressing myelination for assessment preterm neonatal brain maturation based on novel automatic segmentation method for myelin-like signals on T₂-weighted magnetic resonance images. Firstly we define a segmentation protocol for myelin-like signals. We then develop an expectation-maximization framework to obtain the automatic segmentations of myelin-like signals with explicit class for partial volume voxels whose locations are configured in relation to the composing pure tissues via second-order Markov random fields. The proposed segmentation achieves high Dice overlaps of 0.83 with manual annotations. The automatic segmentations are then used to track volumes of myelinated tissues in the regions of the central brain structures and brainstem. Finally, we construct a spatio-temporal growth models for myelin-like signals, which allows us to predict gestational age at scan in preterm infants with root mean squared error 1.41 weeks.