Install FSL, R and R-Studio [ubuntu 16.04 LTS]

FSL_instructions.txt

# Install Ubuntu on VM - shared folder enabled

# Install Guest Addition Disk
    /media/username/VBox_GAs_5.2.6\VBoxLinuxAdditions.run

# Update packages
    apt-get update
    
# Grant access to user to access shared folder
    adduser $username vboxsf       # needs reboot

# Install Python
    apt-get -y install python
    
# Install FSL
    # 1. Download fslinstaller.py via https://fsl.fmrib.ox.ac.uk/fsldownloads_registration
    # 2. python fslinstaller.py
    
echo "
FSLDIR=/usr/local/fsl
. \$FSLDIR/etc/fslconf/fsl.sh
PATH=\$FSLDIR/bin:\$PATH
export FSLDIR PATH" >> ~/.profile

# Install R and required packages for installing devtools
    apt-get -y install r-base r-base-dev libssl-dev libcurl4-openssl-dev
  
# Install neuroimaging packages in R:
    R -e '
    if (!require(devtools)) {
        install.packages("devtools")
    };
    install.packages("oro.nifti");
    install.packages("oro.dicom");
    devtools::install_github("muschellij2/fslr");
    devtools::install_github("stnava/ITKR");
    devtools::install_github("stnava/ANTsR");
    devtools::install_github("muschellij2/extrantsr");'
    
# Install R-Studio
    apt-get -y install gdebi-core    # install gdebi to install rstudio with
    wget $rstudio_URL             # download rstudio installation file -> find latest at https://www.rstudio.com/products/rstudio/download/#download
    gdebi -n $downloaded_file     # install rstudio
    rm $downloaded_file           # delete installation file