FSLmaths - Shell/Bash

FSLmaths is a command-line tool that is a part of the FSL (FMRIB Software Library) neuroimaging software package. It is a powerful tool for image processing and manipulation, and can be used for a wide variety of tasks related to neuroimaging research.

Installation

FSL is free and open-source software, and can be installed on Linux, macOS, and Windows. Follow the instructions on the FSL website for installation on your operating system: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation

Usage

The basic syntax for FSLmaths is as follows:

fslmaths input_image -operation value output_image

where input_image is the name of the input image file, -operation is the type of image operation to apply, value is the value to use for the operation, and output_image is the name of the output image file.

For example, to apply a threshold operation to an image, you could use the following command:

fslmaths input_image -thr 0.5 output_image

This would set all values below 0.5 to 0, and all values above 0.5 to 1.

FSLmaths supports many different kinds of operations, including mathematical operations (addition, subtraction, multiplication, and division), image thresholding, smoothing, and more. See the FSLmaths documentation for a full list of operations.

Example

Here is an example of using FSLmaths to apply a smoothing operation to an input image:

fslmaths input_image -s 2.0 output_image

This command would apply a 2mm Gaussian smoothing kernel to the input image, and save the output as output_image.

Conclusion

FSLmaths is a versatile and powerful tool for image processing and manipulation, and is an essential part of the FSL neuroimaging software package. With a variety of image operations available, it is well-suited for a wide range of neuroimaging research tasks.