brain extraction in python
Project description
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 pypispheresphere
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:
brainextractor --help
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