Image processing steps for acquiring skull-stripped CT (ssCT) and intensity-transformed CT (itCT) templates.

<p>(a) Inhomogeneity correction and segmentation of MR, (b) creation of whole brain and CSF masks, (c) skull-stripping of inhomogeneity-corrected MR, (d) spatial normalization of skull-stripped MR to MNI template for skull-stripped MR, (e) spatial normalization of masks by applying normalization parameter, (f) creation of probabilistic maps for whole brain and CSF by averaging tissue masks, (g) coregistration of CT to inhomogeneity-corrected MR, (h) creation of skull mask, (i) spatial normalization of skull mask, (j) creation of probabilistic map for skull, (k) spatial normalization of coregistered CT, (l) creation of whole CT template by averaging, (m) creation of template mask for scalp-stripping, (n) spatial normalization of CT to whole CT template, (o) inverse normalization of template mask for scalp-stripping to create individual mask for scalp-stripping, (p) creation of scalp-stripped CT by applying mask, (q) segmentation of scalp-stripped CT into three tissue type by using probabilistic maps, (r) creation of ssCT by applying mask for whole brain segment, (s) coregistration of ssCT to MR by applying parameter coregistering original CT to MR, (t) spatial normalization of coregistered ssCT, (u) creation of ssCT template by averaging, (v) intensity transformation of original CT, (w) coregistration of itCT to MR, (x) spatial normalization of coregistered itCT, (y) creation of itCT template by averaging, and (z) spatial normalization of individual ssCT and itCT to specific CT templates. The processing steps inside the red (ssCT) and blue (itCT) dashed lines represent the image processing steps required for the spatial normalization of CT images with created CT templates.