1 Instructors

1.1 Schedule

All the PDF slides are located in a zip file here.

title slides pdf_slides rcode source
Introduction and R Slides PDF Slides R Code Source
General R (not covered at ENAR) Slides PDF Slides R Code Source
Imaging Packages in R Slides PDF Slides R Code Source
Visualization of Images Slides PDF Slides R Code Source
Inhomogeneity Correction Slides PDF Slides R Code Source
Brain Extraction/Segmentation Slides PDF Slides R Code Source
Image Registration Slides PDF Slides R Code Source
Tissue-Class Segmentation Slides PDF Slides R Code Source
Intensity Normalization Slides PDF Slides R Code Source
Segmentation of MS Lesions Slides PDF Slides R Code Source
Image Harmonization Slides PDF Slides R Code Source
Starting with Raw (DICOM) Data (not covered) Slides PDF Slides R Code Source

2 Materials

All materials for this course are located at: https://github.com/muschellij2/imaging_in_r

We have created a function cheatsheet for all the functions we will call during the course.

2.2 RStudio Server

The server is located at: http://johnmuschelli.com/rstudio_server.html and you will be given a username and a password.

The code to make the server is located at: https://github.com/muschellij2/rneuro/blob/master/ms_rstudio_droplet.sh

2.2.1 Local R Setup

We have provided a set of instructions to install all the requirements on your local system after the tutorial at: http://johnmuschelli.com/imaging_in_r/installing_everything_locally/.

2.2.1.1 Installation

This script should install the packages locally for Mac OSX/Linux/Windows:

if (!"devtools" %in% installed.packages()) {
install.packages("devtools")
}
if (!"ms.lesion" %in% installed.packages()) {
devtools::install_github("muschellij2/ms.lesion")
}
source("https://neuroconductor.org/neurocLite.R")
pkgs = c("neurobase", "fslr", "dcm2niir","divest",
"RNifti", "oro.dicom",
"oro.nifti", "WhiteStripe", "neurohcp", "papayar",
"papayaWidget", "oasis", "kirby21.t1")
neuro_install(pkgs)
# data for whitestripe
library(dcm2niir); install_dcm2nii()
library(WhiteStripe); download_img_data()

In order to use fslr with FSL (availabel for Mac OSX and Linux only), you must install FSL.

These packages only work for Mac OSX and Linux:

neuro_install(c("ITKR", "ANTsRCore", "ANTsR", "extrantsr"),
upgrade_dependencies = FALSE)

This is a package for MALF (multi-atlas label fusion), but is a very large package, so only download it if you are going to do MALF:

neuro_install("malf.templates")

3 Course Description

In this tutorial, we will provide tutorials on how to use R for structural magnetic resonance imaging (MRI) analysis. We will show how to perform entire image analysis in R, from the scans in raw image format to the statistical analysis after image preprocessing, with an emphasis on reproducibility by using a single programming language. This course will use a real multiple sclerosis dataset and will show the steps of going from the raw image files to performing multiple sclerosis lesion classification with a number of classifiers entirely in R. In this hands-on tutorial, attendees will be given instructions for setup and data before the course, so that they are able to follow along and perform the analysis during the tutorial. The topics to be cover in the course are as follows:

• Introduction to the Statistical Software R
• Visualization of Images and Image Data
• Inhomogeneity Correction
• Brain Extraction
• Image Segmentation
• Coregistration Within and Between MRI Studies
• Intensity Normalization