Figure 2.

Template-based brain localization and extraction from clinical MR images. In each stack s, the initial global alignment and position of the fetal brain (global rigid transformation ${\widehat{\mathbf{T}}}_s^1$) is estimated using a block matching approach: Slices of the age-matched template image are matched to slices in the fetal brain MRI stack. It corresponds to the brain localization step. The contour of the best match is indicated in red. Then, brain masks are obtained through the brain extraction step. It consists of (i) cropping and reorienting the stack to the template space using ${\widehat{\mathbf{T}}}_s^1$, (ii) performing rigid slice-to-template registration to refine the brain localization within the slice and to correct for inter-slice motion (rigid slice-to-template transformation ${\mathbf{T}}_j^2$), (iii) performing a 2D B-Spline deformable registration to take into account anatomical variability between the processed brain and the template brain (deformation field D̂_sj), and (iv) propagating the template brain mask to each slice, using the estimated transformations and deformation field.