Segmentation of the brain using direction-averaged signal of DWI images

Hu Cheng; Sharlene Newman; Maryam Afzali; Shreyas Sanjeev Fadnavis; Eleftherios Garyfallidis

doi:10.1016/j.mri.2020.02.010

Segmentation of the brain using direction-averaged signal of DWI images

Magn Reson Imaging. 2020 Jun:69:1-7. doi: 10.1016/j.mri.2020.02.010. Epub 2020 Feb 20.

Authors

Hu Cheng¹, Sharlene Newman², Maryam Afzali³, Shreyas Sanjeev Fadnavis⁴, Eleftherios Garyfallidis⁵

Affiliations

¹ Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Program of Neuroscience, Indiana University, Bloomington, IN 47405, USA. Electronic address: hucheng@indiana.edu.
² Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Program of Neuroscience, Indiana University, Bloomington, IN 47405, USA.
³ Cardiff University Brain Research Imaging Centre, Cardiff CF24 4HQ, UK.
⁴ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, USA.
⁵ Program of Neuroscience, Indiana University, Bloomington, IN 47405, USA; Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, USA.

PMID: 32088291
DOI: 10.1016/j.mri.2020.02.010

Abstract

Segmentation of brain tissue in diffusion MRI image space has some unique advantages. A novel segmentation method using the direction-averaged diffusion weighted imaging (DWI) signal is proposed. Two images can be obtained from the fitting of the direction-averaged DWI signal as a function of b-value: one with superior contrast between the gray matter and white matter; one with prominent CSF contrast. A pseudo T1 weighted image can be constructed and standard segmentation tools can be applied. The method was tested on the HCP dataset using SPM12, and showed good agreement with segmentation using the T1 weighted image with the same resolution. The Dice score was all greater than 0.88 for GM or WM with full DWI data and very stable against subsampling of the DWI data in number of diffusion directions, number of shells, and spatial resolution.

Keywords: CSF; Diffusion MRI; Direction-averaged; Gray matter; Segmentation; White matter.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Brain / diagnostic imaging*
Cerebral Cortex / diagnostic imaging
Diffusion Magnetic Resonance Imaging*
Gray Matter / diagnostic imaging
Humans
Image Processing, Computer-Assisted / methods*
White Matter / diagnostic imaging

Abstract

Publication types

MeSH terms

Grants and funding