Cortical Thickness Estimation

All code for this document is located at here.

base_fname = "113-01-T1"
orig = file.path("..", 
                 "brain_extraction",
                 paste0(base_fname, "_SS.nii.gz")
)
stub = file.path("..", "tissue_class_segmentation", 
                base_fname)
seg = paste0(stub, "_Seg.nii.gz")
wm_prob = paste0(stub, "_prob_2.nii.gz")
gm_prob = paste0(stub, "_prob_3.nii.gz")

s = antsImageRead(seg)
g = antsImageRead(gm_prob)
w = antsImageRead(wm_prob)
out = kellyKapowski(s = s, g = g, w = w, its = 50, r = 0.025, m = 1.5)
cort = extrantsr::ants2oro(out)

ortho2(cort)

hist(c(cort[cort > 0]), breaks = 2000)

ortho2(cort, cort > 0.1)

ortho2(img, cort)