The goal of ichseg
is to perform preprocessing on computed tomography
(CT) scans, including skull stripping. Computes predictors of
intracerebral hemorrhage (ICH) and uses these to predict a binary
hemorrhage mask from the data.
To cite ichseg
, you can run:
citation("ichseg")
Muschelli J, Sweeney EM, Ullman NL, Vespa P, Hanley DF, Crainiceanu CM
(2017). "PItcHPERFeCT: Primary Intracranial Hemorrhage Probability
Estimation using Random Forests on CT." _NeuroImage: Clinical_, *14*,
379-390.
A BibTeX entry for LaTeX users is
@Article{muschelli2017pitchperfect,
title = {{PItcHPERFeCT}: Primary Intracranial Hemorrhage Probability Estimation using Random Forests on {CT}},
author = {John Muschelli and Elizabeth M Sweeney and Natalie L Ullman and Paul Vespa and Daniel F Hanley and Ciprian M Crainiceanu},
journal = {NeuroImage: Clinical},
volume = {14},
pages = {379--390},
year = {2017},
publisher = {Elsevier},
}
You can install ichseg
from github with:
# install.packages("devtools")
devtools::install_github("muschellij2/ichseg")
These functions require a working installation of FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation), which can be installed via Neurodebian as well: http://neuro.debian.net/pkgs/fsl-complete.html.
In order to segment ICH from an image, use the ich_segment
function:
ichseg::ich_segment(img = "/path/to/ct/scan")