Deep Skull

A DICOM skull stripping command line tool, using the model and weights from CT_BET.

Installation

Clone project:

git clone git@github.com:jdddog/deep-skull.git

Enter deep-skull folder:

cd deep-skull

Create a virtual environment.

virtualenv -p python3.8 venv

Activate your virtual environment.

source venv/bin/activate

Install:

pip install -e .

Set the CUDA device you want to use:

export CUDA_VISIBLE_DEVICES=0

To extract brain for CTs:

deep-skull extract-brain /path/to/nifti ax_CT --num-workers 1

To extract brain for CTAs:

deep-skull extract-brain /path/to/nifti ax_A --num-workers 1

To print help text for the command:

deep-skull extract-brain --help