brainextractor's Introduction

brainextractor

A reimplementation of FSL's Brain Extraction Tool in Python.

Follows the algorithm as described in:

Smith SM. Fast robust automated brain extraction. Hum Brain Mapp.
2002 Nov;17(3):143-55. doi: 10.1002/hbm.10062. PMID: 12391568; PMCID: PMC6871816.

Install

To install, simply use pip to install this repo:

# install from pypi
pip install brainextractor

# install repo with pip
pip install git+https://github.com/vanandrew/brainextractor@main

# install from local copy
pip install /path/to/local/repo

Note that it is recommended to use brainextractor on python 3.7+

Usage

To extract a brain mask from a image, you can call:

# basic usage
brainextractor [input_image] [output_image]

# example
brainextractor /path/to/test_image.nii.gz /path/to/some_output_image.nii.gz

You can adjust the fractional intensity with the -f flag:

# with custom set threshold
brainextractor [input_image] [output_image] -f [threshold]

# example
brainextractor /path/to/test_image.nii.gz /path/to/some_output_image.nii.gz -f 0.4

To view the deformation process, you can use the -w flag to write the surfaces to a file. Then use brainextractor_render to view them:

# writes surfaces to file
brainextractor [input_image] [output_image] -w [surfaces_file]

# load surfaces and render
brainextractor_render [surfaces_file]

# example
brainextractor /path/to/test_image.nii.gz /path/to/some_output_image.nii.gz -w /path/to/surface_file.surfaces

brainextractor_render /path/to/surface_file.surfaces

If you need an explanation of the options at any time, simply run the help: