---

output: github_document

---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r setup, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "",

  fig.path = "man/figures/README-"

)

```

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

<!-- badges: start -->

[![Travis build status](https://travis-ci.com/muschellij2/ichseg.svg?branch=master)](https://travis-ci.com/muschellij2/ichseg)

[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/muschellij2/ichseg?branch=master&svg=true)](https://ci.appveyor.com/project/muschellij2/ichseg)

<!-- badges: end -->

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:

```{r}

citation("ichseg")

```

## Installation

You can install `ichseg` from github with:

```{r gh-installation, eval = FALSE}

# 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:

```{r, eval = FALSE}

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

```