Whole volume brain extraction for multi-centre, multi-disease FLAIR MRI datasets

FLAIR MRI biomarkers of the normal appearing brain matter are related to cognition

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Normal appearing brain matter (NABM) biomarkers in FLAIR MRI are related to cognition.

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NABM texture in FLAIR MRI is correlated to mean diffusivity (MD) in dMRI.

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Analysis conducted on large multicentre FLAIR MRI dataset: 1400 subjects, 87 centers.

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NABM biomarkers vary differently across age and MoCA categories.

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Biomarkers showed differences in patients with AD dementia and vascular disease.

A novel biomarker panel was proposed to quantify macro and microstructural biomarkers from the normal-appearing brain matter (NABM) in multicentre fluid-attenuation inversion recovery (FLAIR) MRI. The NABM is composed of the white and gray matter regions of the brain, with the lesions and cerebrospinal fluid removed. The primary hypothesis was that NABM biomarkers from FLAIR MRI are related to cognitive outcome as determined by MoCA score. There were three groups of features designed for this task based on 1) texture: microstructural integrity (MII), macrostructural damage (MAD), microstructural damage (MID), 2) intensity: median, skewness, kurtosis and 3) volume: NABM to ICV volume ratio. Biomarkers were extracted from over 1400 imaging volumes from more than 87 centres and unadjusted ANOVA analysis revealed significant differences in means of the MII, MAD, and NABM volume biomarkers across all cognitive groups. In an adjusted ANCOVA model, a significant relationship between MoCA categories was found that was dependent on subject age for MII, MAD, intensity, kurtosis and NABM volume biomarkers. These results demonstrate that structural brain changes in the NABM are related to cognitive outcome (with different relationships depending on the age of the subjects). Therefore these biomarkers have high potential for clinical translation. As a secondary hypothesis, we investigated whether texture features from FLAIR MRI can quantify microstructural changes related to how “structured” or “damaged” the tissue is. Based on correlation analysis with diffusion weighted MRI (dMRI), it was shown that FLAIR MRI texture biomarkers (MII and MAD) had strong correlations to mean diffusivity (MD) which is related to tissue degeneration in the GM and WM regions. As FLAIR MRI is routinely collected for clinical neurological examinations, novel biomarkers from FLAIR MRI could be used to supplement current clinical biomarkers and for monitoring disease progression. Biomarkers could also be used to stratify patients into homogeneous disease subgroups for clinical trials, or to learn more about mechanistic development of dementia disease.

A Survey on EEG Signal Processing Techniques and Machine Learning: Applications to the Neurofeedback of Autobiographical Memory Deficits in Schizophrenia

In this paper, a general overview regarding neural recording, classical signal processing techniques and machine learning classification algorithms applied to monitor brain activity is presented. Currently, several approaches classified as electrical, magnetic, neuroimaging recordings and brain stimulations are available to obtain neural activity of the human brain. Among them, non-invasive methods like electroencephalography (EEG) are commonly employed, as they can provide a high degree of temporal resolution (on the order of milliseconds) and acceptable space resolution. In addition, it is simple, quick, and does not create any physical harm or stress to patients. Concerning signal processing, once the neural signals are acquired, different procedures can be applied for feature extraction. In particular, brain signals are normally processed in time, frequency, and/or space domains. The features extracted are then used for signal classification depending on its characteristics such us the mean, variance or band power. The role of machine learning in this regard has become of key importance during the last years due to its high capacity to analyze complex amounts of data. The algorithms employed are generally classified in supervised, unsupervised and reinforcement techniques. A deep review of the most used machine learning algorithms and the advantages/drawbacks of most used methods is presented. Finally, a study of these procedures utilized in a very specific and novel research field of electroencephalography, i.e., autobiographical memory deficits in schizophrenia, is outlined.

Automated Midline Estimation for Symmetry Analysis of Cerebral Hemispheres in FLAIR MRI

To perform brain asymmetry studies in large neuroimaging archives, reliable and automatic detection of the interhemispheric fissure (IF) is needed to first extract the cerebral hemispheres. The detection of the IF is often referred to as mid-sagittal plane estimation, as this plane separates the two cerebral hemispheres. However, traditional planar estimation techniques fail when the IF presents a curvature caused by existing pathology or a natural phenomenon known as brain torque. As a result, midline estimates can be inaccurate. In this study, a fully unsupervised midline estimation technique is proposed that is comprised of three main stages: head angle correction, control point estimation and midline generation. The control points are estimated using a combination of intensity, texture, gradient, and symmetry-based features. As shown, the proposed method automatically adapts to IF curvature, is applied on a slice-to-slice basis for more accurate results and also provides accurate delineation of the midline in the septum pellucidum, which is a source of failure for traditional approaches. The method is compared to two state-of-the-art methods for midline estimation and is validated using 75 imaging volumes (~3,000 imaging slices) acquired from 38 centers of subjects with dementia and vascular disease. The proposed method yields the lowest average error across all metrics: Hausdorff distance (HD) was 0.32 ± 0.23, mean absolute difference (MAD) was 1.10 ± 0.38 mm and volume difference was 7.52 ± 5.40 and 5.35 ± 3.97 ml, for left and right hemispheres, respectively. Using the proposed method, the midline was extracted for 5,360 volumes (~275K images) from 83 centers worldwide, acquired by GE, Siemens and Philips scanners. An asymmetry index was proposed that automatically detected outlier segmentations (which were <1% of the total dataset). Using the extracted hemispheres, hemispheric asymmetry texture biomarkers of the normal-appearing brain matter (NABM) were analyzed in a dementia cohort, and significant differences in biomarker means were found across SCI and MCI and SCI and AD.

Manual segmentation versus semi-automated segmentation for quantifying vestibular schwannoma volume on MRI

Purpose

Management of vestibular schwannoma (VS) is based on tumour size as observed on T1 MRI scans with contrast agent injection. The current clinical practice is to measure the diameter of the tumour in its largest dimension. It has been shown that volumetric measurement is more accurate and more reliable as a measure of VS size. The reference approach to achieve such volumetry is to manually segment the tumour, which is a time intensive task. We suggest that semi-automated segmentation may be a clinically applicable solution to this problem and that it could replace linear measurements as the clinical standard.

Methods

Using high-quality software available for academic purposes, we ran a comparative study of manual versus semi-automated segmentation of VS on MRI with 5 clinicians and scientists. We gathered both quantitative and qualitative data to compare the two approaches; including segmentation time, segmentation effort and segmentation accuracy.

Results

We found that the selected semi-automated segmentation approach is significantly faster (167 s vs 479 s, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p<0.001$$\end{document}p<0.001), less temporally and physically demanding and has approximately equal performance when compared with manual segmentation, with some improvements in accuracy. There were some limitations, including algorithmic unpredictability and error, which produced more frustration and increased mental effort in comparison with manual segmentation.

Conclusion

We suggest that semi-automated segmentation could be applied clinically for volumetric measurement of VS on MRI. In future, the generic software could be refined for use specifically for VS segmentation, thereby improving accuracy.

Electronic supplementary material

The online version of this article (10.1007/s11548-020-02222-y) contains supplementary material, which is available to authorized users.