PMC4406723_01
Structural MRI scans used for segmentation.. Axial (left), coronal (middle), and sagittal (right) views of the T1- (top) and T2-weighted (bottom) structural MRIs. A specific T2-weighted MRI sequence with high nerve contrast optimized to enhance the structures of the ear and eye was also acquired (data not shown).
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T1 and T2 contrasts: the top half of Fig 1 shows the axial, coronal, and sagittal views of MRI head images from a T1-weighted 3D magnetization prepared gradient echo sequence (MPRAGE) at 500 mum isotropic resolution, TR / TE / flip angle: 15.18 ms / 6.96 ms / 8 , field of view (FOV): 240 mm x 240 mm, number of signal averages (NSA): 1. The bottom half of Fig 1 shows the same views from a T2-weighted 3D turbo spin echo (TSE) sequence with low refocusing flip angle sweep at 500 mum isotropic resolution, TR / TE / TE equivalent to standard TSE: 2250 ms / 424 ms / 164 ms, FOV: 240 mm x 240 mm, NSA: 1.
Vasculature information and DTI.. Axial view of maximum intensity projection from the 3D TOF (left) and the 3D PCA (middle) MRA. The TOF was optimized to highlight blood flowing in the cranial direction, i.e., mostly arteries, whereas the velocity window of the PCA was chosen such to highlight mostly veins. On the right an axial view of the principal eigenvector map is shown. In the color-coded fiber map, red, green, and blue represent the principal diffusion directions. It is possible to distinguish the corpus callosum in red with its fibers running mostly in left-right direction and the internal capsule bundle in blue with fibers running mostly in superior-inferior direction. Diffusion imaging is not directly used for the segmentation and generation of the anatomical model, but it provides anisotropic electrical properties of the tissues for electromagnetic applications and nerve orientation.
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TR / TE / flip angle: 19.09 ms / 7.06 ms / 10 , FOV: 230 mm x 230 mm, NSA: 1, SENSE undersampling factor: 2 were employed. Fig 2 shows axial maximum intensity projections from the 3D TOF (left) and the 3D PCA (middle) volumes. To assess the microstructure of the brain, a diffusion-weighted single-shot spin-echo echo-planar-imaging (DW SSh-SE-EPI) sequence was acquired, with 32 diffusion orientations (b-values 0 and 800 s/mm2), at 1.5 mm x 1.5 mm x 2.5 mm resolution:, TR / TE: 7121 ms / 85 ms, FOV: 240 mm x 240 mm, NSA: 5, SENSE under sampling factor: 3, spectral fat saturation pre-pulse. An axial view of the principal eigenvector map is given in Fig 2 (right).
T1- and T2-weighted MRI registration.. Sagittal view of the registered and integrated T1- and T2-weighted MRIs. The contrast between WM, e.g., corpus callosum, and GM signals is higher in T1, while the CSF, e.g., ventricle, is enhanced in T2. The tissue segmentation was performed by reaping the benefits of both MRI datasets.
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Fig 3 shows a sagittal view of the registered and integrated T1- and T2-weighted MRIs.