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)
1 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 source
abind 1.4-5 2016-07-21 [2] CRAN (R 4.0.0)
animation * 2.6 2018-12-11 [2] CRAN (R 4.0.0)
ANTsR * 0.5.6.1 2020-06-01 [2] Github (ANTsX/ANTsR@9c7c9b7)
ANTsRCore * 0.7.4.6 2020-07-07 [2] Github (muschellij2/ANTsRCore@61c37a1)
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [2] CRAN (R 4.0.0)
cachem 1.0.4 2021-02-13 [1] CRAN (R 4.0.2)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
cli 2.3.0 2021-01-31 [1] CRAN (R 4.0.2)
codetools 0.2-18 2020-11-04 [1] CRAN (R 4.0.2)
colorout * 1.2-2 2020-06-01 [2] Github (jalvesaq/colorout@726d681)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.2)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.2)
desc 1.2.0 2020-06-01 [2] Github (muschellij2/desc@b0c374f)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
dplyr * 1.0.4 2021-02-02 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [2] CRAN (R 4.0.0)
evaluate 0.14 2019-05-28 [2] CRAN (R 4.0.0)
extrantsr * 3.9.13.1 2020-09-03 [2] Github (muschellij2/extrantsr@00c75ad)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [2] CRAN (R 4.0.2)
fslr * 2.25.0 2021-02-16 [1] local
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.2)
ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 4.0.2)
git2r 0.28.0 2021-01-11 [1] Github (ropensci/git2r@4e342ca)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [2] CRAN (R 4.0.0)
highr 0.8 2019-03-20 [2] CRAN (R 4.0.0)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
ITKR 0.5.3.3.0 2021-02-15 [1] Github (stnava/ITKR@ea0ac19)
kirby21.base * 1.7.4 2020-10-01 [1] local
kirby21.fmri * 1.7.0 2018-08-13 [2] CRAN (R 4.0.0)
kirby21.t1 * 1.7.3.2 2021-01-09 [1] local
knitr 1.31 2021-01-27 [1] CRAN (R 4.0.2)
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
matlabr 1.6.0 2020-07-01 [2] local
Matrix 1.3-2 2021-01-06 [1] CRAN (R 4.0.2)
matrixStats * 0.58.0 2021-01-29 [1] CRAN (R 4.0.2)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.2)
mgcv 1.8-33 2020-08-27 [1] CRAN (R 4.0.2)
munsell 0.5.0 2018-06-12 [2] CRAN (R 4.0.0)
neurobase * 1.31.0 2020-10-07 [1] local
nlme 3.1-152 2021-02-04 [1] CRAN (R 4.0.2)
oro.nifti * 0.11.0 2020-09-04 [2] local
pillar 1.4.7 2020-11-20 [1] CRAN (R 4.0.2)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.0.0)
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plyr 1.8.6 2020-03-03 [2] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.0.0)
processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.2)
ps 1.5.0 2020-12-05 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [2] CRAN (R 4.0.0)
R.matlab 3.6.2 2018-09-27 [2] CRAN (R 4.0.0)
R.methodsS3 * 1.8.1 2020-08-26 [1] CRAN (R 4.0.2)
R.oo * 1.24.0 2020-08-26 [1] CRAN (R 4.0.2)
R.utils * 2.10.1 2020-08-26 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
RColorBrewer * 1.1-2 2014-12-07 [2] CRAN (R 4.0.0)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.2)
RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.0.2)
remotes 2.2.0 2020-07-21 [2] CRAN (R 4.0.2)
reshape2 * 1.4.4 2020-04-09 [2] CRAN (R 4.0.0)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2)
rmarkdown * 2.6 2020-12-14 [1] CRAN (R 4.0.2)
RNifti * 1.3.0 2020-12-04 [1] CRAN (R 4.0.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
scales 1.1.1 2020-05-11 [2] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 4.0.0)
spm12r * 2.8.2 2021-01-11 [1] local
stapler 0.7.2 2020-07-09 [2] Github (muschellij2/stapler@79e23d2)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
stringr * 1.4.0 2019-02-10 [2] CRAN (R 4.0.0)
testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.2)
tibble 3.0.6 2021-01-29 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [2] CRAN (R 4.0.0)
usethis * 2.0.1 2021-02-10 [1] CRAN (R 4.0.2)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.2)
WhiteStripe 2.3.2 2019-10-01 [2] CRAN (R 4.0.0)
withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.2)
xfun 0.21 2021-02-10 [1] CRAN (R 4.0.2)
yaml * 2.2.1 2020-02-01 [2] CRAN (R 4.0.0)
zoo * 1.8-8 2020-05-02 [2] CRAN (R 4.0.0)
[1] /Users/johnmuschelli/Library/R/4.0/library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library