Multi-label brain segmentation from brain magnetic resonance imaging (MRI) provides valuable structural information for most neurological analyses. Due to the complexity of the brain segmentation algorithm, it could delay the delivery of neuroimaging findings. Therefore, we introduce Split-Attention U-Net (SAU-Net), a convolutional neural network with skip pathways and a split-attention module that segments brain MRI scans. The proposed architecture employs split-attention blocks, skip pathways with pyramid levels, and evolving normalization layers. For efficient training, we performed pre-training and fine-tuning with the original and manually modified FreeSurfer labels, respectively. This learning strategy enables involvement of heterogeneous neuroimaging data in the training without the need for many manual annotations. Using nine evaluation datasets, we demonstrated that SAU-Net achieved better segmentation accuracy with better reliability that surpasses those of state-of-the-art methods. We believe that SAU-Net has excellent potential due to its robustness to neuroanatomical variability that would enable almost instantaneous access to accurate neuroimaging biomarkers and its swift processing runtime compared to other methods investigated.

Objective Alzheimer’s disease (AD) is the most common type of dementia and the prevalence rapidly increased as the elderly population increased worldwide. In the contemporary model of AD, it is regarded as a disease continuum involving preclinical stage to severe dementia. For accurate diagnosis and disease monitoring, objective index reflecting structural change of brain is needed to correctly assess a patient’s severity of neurodegeneration independent from the patient’s clinical symptoms. The main aim of this paper is to develop a random forest (RF) algorithm-based prediction model of AD using structural magnetic resonance imaging (MRI).Methods We evaluated diagnostic accuracy and performance of our RF based prediction model using newly developed brain segmentation method compared with the Freesurfer’s which is a commonly used segmentation software.Results Our RF model showed high diagnostic accuracy for differentiating healthy controls from AD and mild cognitive impairment (MCI) using structural MRI, patient characteristics, and cognitive function (HC vs. AD 93.5%, AUC 0.99; HC vs. MCI 80.8%, AUC 0.88). Moreover, segmentation processing time of our algorithm (<5 minutes) was much shorter than of Freesurfer’s (6–8 hours).Conclusion Our RF model might be an effective automatic brain segmentation tool which can be easily applied in real clinical practice.

White-matter hyperintensity (WMH) is a primary biomarker for small-vessel cerebrovascular disease, Alzheimer’s disease (AD), and others. The association of WMH with brain structural changes has also recently been reported. Although fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) provide valuable information about WMH, FLAIR does not provide other normal tissue information. The multi-modal analysis of FLAIR and T1-weighted (T1w) MRI is thus desirable for WMH-related brain aging studies. In clinical settings, however, FLAIR is often the only available modality. In this study, we thus propose a semi-supervised learning method for full brain segmentation using FLAIR. The results of our proposed method were compared with the reference labels, which were obtained by FreeSurfer segmentation on T1w MRI. The relative volume difference between the two sets of results shows that our proposed method has high reliability. We further evaluated our proposed WMH segmentation by comparing the Dice similarity coefficients of the reference and the results of our proposed method. We believe our semi-supervised learning method has a great potential for use for other MRI sequences and will encourage others to perform brain tissue segmentation using MRI modalities other than T1w.

Amyloid positron emission tomography (PET) scan is clinically essential for the non-invasive assessment of the presence and spatial distribution of amyloid-beta deposition in subjects with cognitive impairment suspected to have been a result of Alzheimer’s disease. Quantitative assessment can enhance the interpretation reliability of PET scan; however, its clinical application has been limited due to the complexity of preprocessing. This study introduces a novel deep-learning-based approach for SUVR quantification that simplifies the preprocessing step and significantly reduces the analysis time. Using two heterogeneous amyloid ligands, our proposed method successfully distinguished standardized uptake value ratio (SUVR) between amyloidosis-positive and negative groups. The proposed method’s intra-class correlation coefficients were 0.97 and 0.99 against PETSurfer and PMOD, respectively. The difference of global SUVRs between the proposed method and PETSurfer or PMOD were 0.04 and −0.02, which are clinically acceptable. The AUC-ROC exceeded 0.95 for three tools in the amyloid positive assessment. Moreover, the proposed method had the fastest processing time and had a low registration failure rate (1%). In conclusion, our proposed method calculates SUVR that is consistent with PETSurfer and PMOD, and has advantages of fast processing time and low registration failure rate. Therefore, PET quantification provided by our proposed method can be used in clinical practice.

Brain segmentation of stroke patients can facilitate brain modeling for electrical non-invasive brain stimulation, a therapy for stimulating brain function using an electric current. However, it remains challenging owing to its time-consuming, labor-dependent, and complicated pipeline. In addition, conventional tools that define lesions into one region rather than distinguishing between the stroke-affected regions and cerebrospinal fluid can lead to inaccurate treatment results. In this study, we first define a novel stroke-affected region as a detailed sub-region of the conventionally defined lesion. Subsequently, a novel comprehensive framework is proposed to segment head-brain and fine-level stroke-affected regions for normal controls and chronic stroke patients. The proposed framework consists of a time-efficient and precise deep learning-based segmentation model. The experiment results indicate that the proposed method perform better than the conventional deep learning-based segmentation model in terms of the evaluation metrics. The proposed method would be a valuable addition to brain modeling for non-invasive neuromodulation.

Normative brain magnetic resonance imaging (MRI) is essential to interpret the state of an individual’s brain health. However, a normative study is often expensive for small research groups. Although several attempts have been made to establish brain MRI norms, the focus has been limited to certain age ranges. This study aimed to establish East Asian normative brain data using multi-site MRI and determine the robustness of these data for clinical research. Normative MRI was gathered covering a wide range of cognitively normal East Asian populations (age: 18–96 years) from two open sources and three research sites. Eight sub-regional volumes were extracted in the left and right hemispheres using an in-house deep learning-based tool. Repeated measure consistency and multicenter reliability were determined using intraclass correlation coefficients and compared to a widely used tool, FreeSurfer. Our results showed highly consistent outcomes with high reliability across sites. Our method outperformed FreeSurfer in repeated measure consistency for most structures and multicenter reliability for all structures. The normative MRI we constructed was able to identify sub-regional differences in mild cognitive impairments and dementia after covariate adjustments. Our investigation suggests it is possible to provide a sound normative reference for neurodegenerative or aging research.