Computational protocol: Atlas guided volumetric diffuse optical tomography enhanced by generalized linear model analysis to image risk decision making responses in young adults

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Protocol publication

[…] Pre-processed fNIRS data were then further processed with brain atlas-guided tomographic image reconstruction to form volumetric images at different temporal points. The MRI-based human brain atlas used in this study was the current standard Montreal Neurological Institution (MNI) template, known as International Consortium for Brain Mapping (ICBM) 152 MNI []. ICBM152 MNI template was obtained by averaging the MRI scans of 152 normal subjects (a). Each MRI scan was normalized to MNI space using nine parameter affine transformations. ICBM152 MNI template is freely available at ICBM 2009c Nonlinear Asymmetric template was selected to generate the head model for this study. Files included T1-weighted, T2-weighted and proton density-weighted images. The spatial resolution of the ICBM152 template was 1 mm × 1 mm × 1 mm as a voxel size with 229 × 193 × 193 voxels. ICBM152 template was then converted to an ANALYZED format using ITK-SNAP [] which is also freely available ( Further image analysis was performed in MATLAB (The MathWorks, Natick, MA).Based on MR images, four regions of interest (ROIs), namely, scalp, skull, gray matter, and white matter, were identified and segmented in this study. A binary mask of the head was made and included in the ICBM template file so that the boundary of scalp could be extracted. Binary masks of skull, gray matter, and white matter were also generated after boundaries of scalp, skull, gray, and white matters were extracted from MR images, as shown in b. After binary masks were obtained, the segmented 2D images were then stacked together to generate 3D volume models (see a–d). Three-dimensional finite element model (FEM) meshes (see e–h) were then generated by a MATLAB-based mesh generator, iso2mesh ( This mesh model contained approximate 2 × 105 nodes, which corresponded to approximately 106 linear tetrahedral elements. Each node was labeled by one of the four ROIs, and all the nodes were assigned with specific tissue optical properties, as listed in Table , which are found in published literature [] for both wavelengths. […]

Pipeline specifications

Software tools ITK-SNAP, iso2mesh
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Diseases