FSL BET - Shell-Bash

FSL BET (Brain Extraction Tool) is a popular image segmentation tool used for brain extraction. It is a command-line tool in the FMRIB Software Library (FSL) and is available for use on Linux, Mac OS X, and Windows.

Installation

To install FSL, follow the instructions on the official FSL website. Once FSL is installed, FSL BET can be run from the command line.

Usage

The basic usage of FSL BET is:

fsl bet <input> <output> [options]

Where <input> is the input file and <output> is the desired output file. There are various options that can be specified to control the parameters of the brain extraction algorithm. Some common options are:

• -f: fractional intensity threshold (0->1); default=0.5
• -g: vertical gradient in fractional intensity threshold (-1->1); default=0
• -m: apply threshold mask to output brain image and set background to zero; default=off
• -n: don't generate segmented brain image output; default=on

Example

Here's an example of running FSL BET on a file called T1.nii.gz:

fsl bet T1.nii.gz T1_brain.nii.gz -f 0.5 -g 0.2

This will create a file called T1_brain.nii.gz that contains the brain extracted from the T1.nii.gz file. The -f option sets the fractional intensity threshold to 0.5 and the -g option sets the vertical gradient to 0.2.

Conclusion

FSL BET is a powerful tool for brain extraction and is widely used in neuroimaging research. With its many options for fine-tuning parameters, it can be a valuable tool for analyzing MRI data.