Automatic segmentation of true color sectioned images using FMRIB Software Library: First trial in brain, gray matter, and white matter

Abstract

Three-dimensional (3D) models of the brain made from magnetic resonance images (MRI) are used in various medical fields. 3D models assembled from grayscale color and low-resolution can be complemented with true color sectioned images of the Visible Korean. The purpose of this study is to apply the MRI automatic segmentation technique to the sectioned images. 3D models of the sectioned images, which have true color and high resolution, can be produced without manual segmentation. The Brain Extraction Tool and the Automated Segmentation Tool of the FMRIB Software Library (FSL) were chosen for automatic segmentation. Using those tools, true color sectioned images were reconstructed from gray 3D models of brain, gray matter, and white matter. Color 3D models of those structures were generated from the gray 3D models using MRIcroGL. The color 3D models made from the sectioned images revealed details of brain anatomy that could not be observed on the 3D models from MRI. This trial suggests that convergence of the MRI segmentation technique with color sectioned images is a time-efficient method for producing color 3D models of various structures. In future, the method of this study will be used for various sectioned images of cadavers. The resulting color sectioned images and 3D models will be made available to other researchers.

Gray Matter Volume Abnormality in Chronic Pain Patients With Depressive Symptoms: A Systemic Review and Meta-Analysis of Voxel-Based Morphometry Studies

“…All the above analysis was repeated in subgroups. The visualization of changed GMV was performed with the MRIcroGL software https://www.nitrc.org/plugins/mwiki/index.php/mricrogl:MainPage/home ( Chung and Park, 2019 , 2020 ; Kumral et al, 2021 ; Park and Jung, 2021 ).…”

Elucidating Multimodal Imaging Patterns in Accelerated Brain Aging: Heterogeneity through a Discriminant Analysis Approach Using the UK Biobank Dataset

“…This process generated a version of the ROIs in the native space, facilitating precise masking within the segmentation framework. Extraction of cortical thickness from cortical regions involved the meticulous implementation of the established FreeSurfer parcellation scheme [33]. This scheme, grounded in the Desikan-Killiany atlas, comprehensively delineates cortical domains across both hemispheres, encompassing a total of 68 discrete regions (UKB ID: 25755-26788, 26856-26889).…”

Understanding the Temporal Dynamics of Accelerated Brain Aging and Resilient Brain Aging: Insights from Discriminative Event-Based Analysis of UK Biobank Data

“…Volume quantification was carefully performed using the FMRIB software library (FSL, version 5.0.10), which is accessible via the platform (http://fsl.fmrib.ox.ac.uk/fsl, accessed on 12 March 2022). Additionally, the FMRIB's automated segmentation tool (FAST, version FAST3) was deployed to derive a total of 139 IDPs (ROIs) [28]. The cortical thickness specific to the ROIs was obtained from the FreeSurfer anatomical parcellation [29], utilizing the Desikan-Killiany Atlas [30] for cortical regions, identifying 68 ROIs, with 34 in each hemisphere.…”