Skip to content

Portable and lightweight brain segmentation in the terminal!

License

Notifications You must be signed in to change notification settings

neuroneural/brainchop-cli

Repository files navigation

BrainChop

BrainChop is a lightweight tool for brain segmentation that runs on pretty much everything.


Installation

You can install BrainChop using pip:

pip install brainchop

Usage

To use BrainChop, run the following command:

brainchop input.nii.gz -o output.nii.gz

Docker

You can also install BrainChop using docker

git clone git@github.com:neuroneural/brainchop-cli.git
cd brainchop-cli
docker build -t brainchop .

Then to run, use

docker run --rm -it --device=nvidia.com/gpu=all -v [[output directory]]:/app brainchop [[input nifti file]] -o [[output nifti file]]

On some systems (like recent 25.05 nixos), the docker run command will need to be prepended with

docker run --rm -it --device=nvidia.com/gpu=all

Where:

  • input.nii.gz is your input NIfTI file
  • output.nii.gz is the desired output file name

Requirements

  • Python 3.6+
  • tinygrad : our tiny and portable (but powerful) ML inference engine
  • numpy : basic tensor operations
  • nibabel : to read nifti files
  • requests : to download models

License

This project is licensed under the MIT License.

About

Portable and lightweight brain segmentation in the terminal!

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published