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Cortical Thickness Estimation
John Muschelli
2021-02-16
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)