Installation

QuIDBBIDS is a MATLAB package that can be installed on Linux, Windows, and macOS systems, provided the following requirements are met.

Requirements:

Installing QuIDBBIDS

The recommended installation method is via Git. This allows you to easily obtain a specific release (main branch) or the latest development version (dev branch; see the contributing guide <https://github.com/Donders-Institute/quidbbids/blob/dev/CONTRIBUTING.rst>`__).

To clone QuIDBBIDS and its dependencies, run:

git clone --recurse-submodules https://github.com/Donders-Institute/QuIDBBIDS.git

This will create a folder named QuIDBBIDS in your current directory.

To install a specific versioned release, list available tags and check out the desired one, for example:

cd QuIDBBIDS
git tag                        # List available release versions (e.g., v1.0.0, v1.0.1, v1.1.0)
git checkout v1.0.1            # Check out a specific (stable) release version
git switch -c dev origin/dev   # Check out the latest (unstable) development code

And to update the dev branch:

git switch dev                 # Check out your dev branch
git pull                       # Get the latest code
qb.resetconfig()               # Update the QuIDBBIDS settings to latest format (may be required after updates)

Then, in MATLAB, add the cloned QuIDBBIDS folder (without subfolders) to your MATLAB path.

Note

If not present, running QuIDBBIDS will install a default configuration file in your home directory, named ~/.quidbbids/v#.#.#/config_default.json. You can modify this file to change default settings or reset them back to factory defaults by running qb.resetconfig() in MATLAB.

Installing dependencies

If you have cloned QuIDBBIDS with --recurse-submodules you already have SEPIA in your QuIDBBIDS dependencies subfolder. Alternatively, you can install the QuIDBBIDS dependencies manually, as listed here.

Unfortunately, not all (sub)dependencies are available on as git repositories, which makes that you still need to install some of SEPIA’s dependencies manually:

  1. CompileMRI

  2. SEGUE

  3. TKD/iterTik/dirTik

As a follow up, edit sepia/SpecifyToolboxesDirectory.m accordingly. More detailed information on installing SEPIA and its dependencies can be found here.

Updating QuIDBBIDS

If you installed QuIDBBIDS using Git, navigate to your local repository and run:

git pull --tags --recurse-submodules

This updates QuIDBBIDS and all dependencies to the latest version on the current branch. To update to a specific release tag instead, use:

git tag                        # List available versions (e.g., v1.0.0, v1.0.1, v1.1.0)
git checkout v1.1.0            # Check out a specific version
git submodule update --init --recursive