This repository is adapted from TotalSegmentator

SkinSegmentator works on Ubuntu, Mac, and Windows and on CPU and GPU.

Install dependencies:

• Python >= 3.9
• Pytorch >= 2.0.0

Install SkinSegmentator

pip install skinsegmentator

SkinSegmentator -i mr.nii.gz -o segmentations

Note: A Nifti file or a folder with all DICOM slices of one patient is allowed as input

Note: If you run on CPU use the option --fast to greatly improve runtime.

Note: This is not a medical device and is not intended for clinical usage.

You can run SkinSegmentator via Python:

import nibabel as nib
from skinsegmentator.python_api import skinsegmentator

if __name__ == "__main__":
    input_path = 'test/Validation_T1_001_0000.nii.gz'
    output_path = 'test/skin.nii.gz'
    # option 1: provide input and output as file paths
    skinsegmentator(input_path, output_path) 

    input_path = 'test/Validation_T1_001_0000.nii.gz'
    output_dir = 'test/'
    # option 2: provide input file path and output dir
    skinsegmentator(input_path, output_dir) 

    # option 3: provide input and output nifti image objects
    input_img = nib.load(input_path)
    output_img = skinsegmentator(input_img)
    nib.save(output_img, output_path)

You can see all available arguments here. Running from within the main environment should avoid some multiprocessing issues.

pip install git+https://github.com/reubendo/SkinSegmentator.git

ITK loading Error When you get the following error message

ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition was found!

you should do

pip install SimpleITK==2.0.2

Alternatively you can try

fslorient -copysform2qform input_file
fslreorient2std input_file output_file

TODO