Reg

Reg is a tool to perform non-linear image registration on 4D volumes in .mat format using the FMRIB’s Software Library (FSL) fnirt tool.

Installation

Reg

The latest version of Reg can be downloaded here on GitHub. Alternatively, you can also download it from the terminal with the following command:

> git clone https://github.com/sxg/Reg.git

Once downloaded, navigate to the folder containing Reg, and run the following command from the terminal to install it:

> pip3 install ./Reg

FSL

Since Reg uses FSL, it must be installed as well. Specific installation instructions are available on FSL’s website.

Usage

Full details on all of Reg’s features and options are described in the help message:

> reg --help

However, some of the options will be described here.

Name

Aside from the .mat to be registered, this is the only required input. name is the name of the image dataset within the .mat file that will be registered. An example file and corresponding dataset is shown here in MATLAB:

> reg --name images dataset.mat

FNIRT Path

This parameter specifies where FSL’s fnirt tool is installed. The default installation path is /usr/local/fsl/bin/fnirt. If left unspecified, Reg will default to this path. If your fnirt tool is located elsewhere, you must specify that here. You can find the location of fnirt with this command:

> which fnirt
/usr/bin/fsl/fnirt

In this case, fnirt is not in the default location. When running Reg, fnirt’s location must be explicitly included:

> reg --name images --fnirt-path /usr/bin/fsl/fnirt dataset.mat

Output Path

The output path tells Reg where to save the registered dataset. If not specified, Reg will save the dataset in a file named registeredImages.mat in your working directory. The .mat extension must be included.

> reg --name images --output-path finalImages.mat dataset.mat

Anchors

Anchor volumes (AKA pre-registered volumes) are volumes that do not need to be registered. This parameter allows you to specify which volumes within the 4D time series dataset are anchor volumes. Reg will register non-anchor volumes to the next anchor volume. If left unspecified, Reg assumes the first volume is the one and only anchor volume. You can specify anchor volumes as a comma-separated list of volume numbers.

For example, let’s say the 5th, 17th, and 26th volumes are to be considered anchors in a dataset containing 50 total volumes. In this case, Reg will use fnirt to register volumes 1–4 to volume 5, volumes 6–16 to volume 17, volumes 18–25 to volume 26, and volumes 27–50 also to volume 26. You can specify this as shown:

> reg --name images --anchors 5,17,26 dataset.mat