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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

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

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