--- a/README.md
+++ b/README.md
@@ -1,65 +1,52 @@
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-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:
-
-    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")
+---
+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-"
+)
+```
+
+
+<!-- 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")
+```
+