Run a brain parcellation deep learning model within 3D Slicer

parcellation_slicer.py

# Paste this code into the Slicer Python console

pip_install('highresnet')

import SampleData
from highresnet.inference import infer
from highresnet.cli.download_oasis import download_oasis

input_path = download_oasis()
loadVolume(input_path)
output_path = input_path.replace('.nii', '_seg.nii')
colors_path = 'Colors.ctbl'
downloadFile('https://raw.githubusercontent.com/fepegar/highresnet/master/GIFNiftyNet.ctbl', colors_path)

infer(
    input_path,
    output_path,
    batch_size=1,
    window_cropping=2,
    volume_padding=10,
    window_size=128,
    cuda_device=0,
    use_niftynet_hist_std=True,
)

labelNode = loadLabelVolume(output_path)
colorNode = loadColorTable(colors_path)
displayNode = labelNode.GetDisplayNode()
displayNode.SetAndObserveColorNodeID(colorNode.GetID())