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)Session Info
devtools::session_info()─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS Catalina 10.15.7
system x86_64, darwin17.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2021-02-16
─ Packages ───────────────────────────────────────────────────────────────────
! package * version date lib
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processx 3.4.5 2020-11-30 [1]
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R.matlab 3.6.2 2018-09-27 [2]
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source
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[1] /Users/johnmuschelli/Library/R/4.0/library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
R ── Package was removed from disk.