README.md

In neuroconductor-devel/ichseg: Intracerebral Hemorrhage Segmentation of X-Ray Computed Tomography (CT) Images

ichseg

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.

Citing

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},
  }

Installation

You can install ichseg from github with:

# install.packages("devtools")
devtools::install_github("muschellij2/ichseg")

Requirements

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.

Prediction

In order to segment ICH from an image, use the ich_segment function:

ichseg::ich_segment(img = "/path/to/ct/scan")

neuroconductor-devel/ichseg documentation built on Sept. 5, 2019, 8:01 p.m.