Nothing
## ----dl_data, eval = FALSE----------------------------------------------------
# library(WhiteStripe)
# download_img_data()
## ----dl_data_run, echo = FALSE, eval = TRUE-----------------------------------
lib.loc = tempdir()
library(WhiteStripe)
download_img_data(lib.loc = lib.loc)
## ----get_data, eval = FALSE---------------------------------------------------
# files = ws_img_data()
## ----get_data_run, echo = FALSE, eval = TRUE----------------------------------
files = ws_img_data(lib.loc = lib.loc)
## ----t1-----------------------------------------------------------------------
library(oro.nifti)
t1 = files[grep("T1", basename(files))]
img = readNIfTI(fname = t1, reorient = FALSE)
## -----------------------------------------------------------------------------
orthographic(img)
## ----hist---------------------------------------------------------------------
vals = img[img > 0]
hist(vals, breaks = 2000)
## ----ws-----------------------------------------------------------------------
ws = whitestripe(img = img, type = "T1", stripped = TRUE)
names(ws)
## ----norm_ws------------------------------------------------------------------
norm = whitestripe_norm(img = img, indices = ws$whitestripe.ind)
## ----print_ws-----------------------------------------------------------------
hist(vals, breaks = 2000)
abline(v = ws$mu.whitestripe, col = "blue")
abline(v = ws$whitestripe, col = "red")
## ----ortho_overlay------------------------------------------------------------
mask = ws$mask.img
mask[mask == 0] = NA
orthographic(x = img, y = mask, col.y = "red")
## ----norm_hist----------------------------------------------------------------
norm_vals = norm[img > 0]
hist(norm_vals, breaks = 2000)
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