Installation

Table of contents
  1. Installation
  2. Requirements
    1. R-environment
    2. Input data
  3. Install R, dependencies and RStudio
    1. Windows
    2. Debian/Ubuntu
    3. Mac
  4. Install the BIDSconvertR

Requirements

R-environment

  • R (4.3.1)
  • RStudio (recent version)
  • R packages installed:
    • ‘devtools’
    • ‘shiny’
    • ‘bidsconvertr’

Input data

The input data must have the following structure:

  • an input folder containing all folders with DICOM data

  • …/subjects/sessions/DICOM
  • one folder per subject, for example: “00001”, “00002”
  • these folders containing the session data, each of which contains the DICOM data
  • …/sessions/subjects/DICOM
  • cross-sectional (at least one folder named ‘crosssectional’ or a custom session name)
  • one folder per session, for example: “session_1”, “session_2”
  • these folders, which contain DICOM data in separate folders for each subject, e.g. “00001”, “00002”
  • if you have any additional file structures, please contact me, so that I can include them.

Install R, dependencies and RStudio

All code was tested with R Version 4.3.1, RTools43, and Tidyverse V 1.3.2.

Windows

Download and install a recent R version (V 4.3.1).

Download and install Rtools43 according to your R-version (V 4.3.1). It is required to install the packages.

Download and install RStudio.

Debian/Ubuntu

To install R and its dependencies, enter the following commands into the terminal.

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo gpg --dearmor -o /usr/share/keyrings/r-project.gpg

echo "deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | sudo tee -a /etc/apt/sources.list.d/r-project.list

sudo apt update

sudo apt install --no-install-recommends r-base

sudo apt install r-base-dev

sudo apt install libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev

Install RStudio.

Then “Right-Click -> Open With ->Software Install” should help in the installation.

Mac

We need some collaborators, who try out the BIDSconvertR on a Mac system. Contact me, if you are interested.

Install the BIDSconvertR

Please install R in accordance with the instructions. From here, copy & paste the following commands into RStudio’s ‘console’ panel.

Known issues:

  • If you are asked to install the package from binary source files select “yes”.
  • If you are asked to update packages, you can skip this step via ‘3’ or update the packages via ‘1’ or ‘2’.
  • If there is a ‘installation of package ‘devtools’ had non-zero exit status’ error message, identify the package (here ‘devtools’) with the error message and install it manually via ‘install.packages(“package_name”)’.

Both packages must be installed only once. The devtools package is required to install packages from Github.

install.packages("shiny")
install.packages("devtools")

Using the command below, you can now install the most recent development version of BIDSconvertR.

devtools::install_github(repo = "bidsconvertr/bidsconvertr")