Automated claustrum segmentation in human brain MRI using deep learning

The claustrum and consciousness: An update

The seminal paper of Crick and Koch (2005) proposed that the claustrum, an enigmatic and thin grey matter structure that lies beside the insular cortex, may be involved in the processing of consciousness. As a result, this otherwise obscure structure has received ever-increasing interest in the search for neural correlates of consciousness. Here we review theories of consciousness and discuss the possible relationship between the claustrum and consciousness. We review relevant experimental evidence collected since the Crick and Koch (2005) paper and consider whether these findings support or contradict their hypothesis. We also explore how future experimental work can be designed to clarify how consciousness emerges from neural activity and to understand the role of the claustrum in consciousness.

Deep learning segmentation results in precise delineation of the putamen in multiple system atrophy

OBJECTIVES

The precise segmentation of atrophic structures remains challenging in neurodegenerative diseases. We determined the performance of a Deep Neural Patchwork (DNP) in comparison to established segmentation algorithms regarding the ability to delineate the putamen in multiple system atrophy (MSA), Parkinson's disease (PD), and healthy controls.

METHODS

We retrospectively included patients with MSA and PD as well as healthy controls. A DNP was trained on manual segmentations of the putamen as ground truth. For this, the cohort was randomly split into a training (N = 131) and test set (N = 120). The DNP's performance was compared with putaminal segmentations as derived by Automatic Anatomic Labelling, Freesurfer and Fastsurfer. For validation, we assessed the diagnostic accuracy of the resulting segmentations in the delineation of MSA vs. PD and healthy controls.

RESULTS

A total of 251 subjects (61 patients with MSA, 158 patients with PD, and 32 healthy controls; mean age of 61.5 ± 8.8 years) were included. Compared to the dice-coefficient of the DNP (0.96), we noted significantly weaker performance for AAL3 (0.72; p < .001), Freesurfer (0.82; p < .001), and Fastsurfer (0.84, p < .001). This was corroborated by the superior diagnostic performance of MSA vs. PD and HC of the DNP (AUC 0.93) versus the AUC of 0.88 for AAL3 (p = 0.02), 0.86 for Freesurfer (p = 0.048), and 0.85 for Fastsurfer (p = 0.04).

CONCLUSION

By utilization of a DNP, accurate segmentations of the putamen can be obtained even if substantial atrophy is present. This allows for more precise extraction of imaging parameters or shape features from the putamen in relevant patient cohorts.

CLINICAL RELEVANCE STATEMENT

Deep learning-based segmentation of the putamen was superior to currently available algorithms and is beneficial for the diagnosis of multiple system atrophy.

KEY POINTS

• A Deep Neural Patchwork precisely delineates the putamen and performs equal to human labeling in multiple system atrophy, even when pronounced putaminal volume loss is present. • The Deep Neural Patchwork-based segmentation was more capable to differentiate between multiple system atrophy and Parkinson's disease than the AAL3 atlas, Freesurfer, or Fastsurfer.

Aberrant claustrum structure in preterm-born neonates: an MRI study

The human claustrum is a gray matter structure in the white matter between insula and striatum. Previous analysis found altered claustrum microstructure in very preterm-born adults associated with lower cognitive performance. As the claustrum development is related to hypoxia-ischemia sensitive transient cell populations being at-risk in premature birth, we hypothesized that claustrum structure is already altered in preterm-born neonates. We studied anatomical and diffusion-weighted MRIs of 83 preterm- and 83 term-born neonates at term-equivalent age. Additionally, claustrum development was analyzed both in a spectrum of 377 term-born neonates and longitudinally in 53 preterm-born subjects. Data was provided by the developing Human Connectome Project. Claustrum development showed increasing volume, increasing fractional anisotropy (FA), and decreasing mean diffusivity (MD) around term both across term- and preterm-born neonates. Relative to term-born ones, preterm-born neonates had (i) increased absolute and relative claustrum volumes, both indicating increased cellular and/or extracellular matter and being in contrast to other subcortical gray matter regions of decreased volumes such as thalamus; (ii) lower claustrum FA and higher claustrum MD, pointing at increased extracellular matrix and impaired axonal integrity; and (iii) aberrant covariance between claustrum FA and MD, respectively, and that of distributed gray matter regions, hinting at relatively altered claustrum microstructure. Results together demonstrate specifically aberrant claustrum structure in preterm-born neonates, suggesting altered claustrum development in prematurity, potentially relevant for later cognitive performance.

Deep learning in neuroimaging data analysis: Applications, challenges, and solutions

Methods for the analysis of neuroimaging data have advanced significantly since the beginning of neuroscience as a scientific discipline. Today, sophisticated statistical procedures allow us to examine complex multivariate patterns, however most of them are still constrained by assuming inherent linearity of neural processes. Here, we discuss a group of machine learning methods, called deep learning, which have drawn much attention in and outside the field of neuroscience in recent years and hold the potential to surpass the mentioned limitations. Firstly, we describe and explain the essential concepts in deep learning: the structure and the computational operations that allow deep models to learn. After that, we move to the most common applications of deep learning in neuroimaging data analysis: prediction of outcome, interpretation of internal representations, generation of synthetic data and segmentation. In the next section we present issues that deep learning poses, which concerns multidimensionality and multimodality of data, overfitting and computational cost, and propose possible solutions. Lastly, we discuss the current reach of DL usage in all the common applications in neuroimaging data analysis, where we consider the promise of multimodality, capability of processing raw data, and advanced visualization strategies. We identify research gaps, such as focusing on a limited number of criterion variables and the lack of a well-defined strategy for choosing architecture and hyperparameters. Furthermore, we talk about the possibility of conducting research with constructs that have been ignored so far or/and moving toward frameworks, such as RDoC, the potential of transfer learning and generation of synthetic data.

Machine learning approaches for biomolecular, biophysical, and biomaterials research

A fluent conversation with a virtual assistant, person-tailored news feeds, and deep-fake images created within seconds-all those things that have been unthinkable for a long time are now a part of our everyday lives. What these examples have in common is that they are realized by different means of machine learning (ML), a technology that has fundamentally changed many aspects of the modern world. The possibility to process enormous amount of data in multi-hierarchical, digital constructs has paved the way not only for creating intelligent systems but also for obtaining surprising new insight into many scientific problems. However, in the different areas of biosciences, which typically rely heavily on the collection of time-consuming experimental data, applying ML methods is a bit more challenging: Here, difficulties can arise from small datasets and the inherent, broad variability, and complexity associated with studying biological objects and phenomena. In this Review, we give an overview of commonly used ML algorithms (which are often referred to as "machines") and learning strategies as well as their applications in different bio-disciplines such as molecular biology, drug development, biophysics, and biomaterials science. We highlight how selected research questions from those fields were successfully translated into machine readable formats, discuss typical problems that can arise in this context, and provide an overview of how to resolve those encountered difficulties.

Efficient Claustrum Segmentation in T2-weighted Neonatal Brain MRI Using Transfer Learning from Adult Scans

Purpose

Intrauterine claustrum and subplate neuron development have been suggested to overlap. As premature birth typically impairs subplate neuron development, neonatal claustrum might indicate a specific prematurity impact; however, claustrum identification usually relies on expert knowledge due to its intricate structure. We established automated claustrum segmentation in newborns.

Methods

We applied a deep learning-based algorithm for segmenting the claustrum in 558 T2-weighted neonatal brain MRI of the developing Human Connectome Project (dHCP) with transfer learning from claustrum segmentation in T1-weighted scans of adults. The model was trained and evaluated on 30 manual bilateral claustrum annotations in neonates.

Results

With only 20 annotated scans, the model yielded median volumetric similarity, robust Hausdorff distance and Dice score of 95.9%, 1.12 mm and 80.0%, respectively, representing an excellent agreement between the automatic and manual segmentations. In comparison with interrater reliability, the model achieved significantly superior volumetric similarity (p = 0.047) and Dice score (p < 0.005) indicating stable high-quality performance. Furthermore, the effectiveness of the transfer learning technique was demonstrated in comparison with nontransfer learning. The model can achieve satisfactory segmentation with only 12 annotated scans. Finally, the model’s applicability was verified on 528 scans and revealed reliable segmentations in 97.4%.

Conclusion

The developed fast and accurate automated segmentation has great potential in large-scale study cohorts and to facilitate MRI-based connectome research of the neonatal claustrum. The easy to use models and codes are made publicly available.