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ichseg <img src="man/figures/logo.png" align="right" height="139" />

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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 (<a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation" class="uri">https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation</a>), which can be installed via Neurodebian as well: <a href="http://neuro.debian.net/pkgs/fsl-complete.html" class="uri">http://neuro.debian.net/pkgs/fsl-complete.html</a>.

Prediction

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

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