This repo contains implementation of various label fusion approaches that can be used to fuse multiple labels.
conda create -n venv_labelFusion python=3.6.5 -y
conda activate venv_labelFusion
pip install LabelFusion# fork to your own repo
git clone ${yourFork_labelFusion_repo_link}
cd LabelFusion
conda create -p ./venv python=3.6.5 -y
conda activate ./venv
pip install -e .
# develop, push
# initiate pull request- Voting (ITK): DOI:10.1016/j.patrec.2005.03.017
- STAPLE (ITK): DOI:10.1109/TMI.2004.830803
- Majority Voting: DOI:10.1007/978-3-319-20801-5_11
- SIMPLE: DOI:10.1109/tmi.2010.2057442
# continue from previous shell
python fusion_run -h
-h, --help show this help message and exit
-inputs INPUTS The absolute, comma-separated paths of labels that need to be fused
-classes CLASSES The expected labels; for example, for BraTS, this should be '0,1,2,4' - not used for STAPLE or ITKVoting
-method METHOD The method to apply; currently available: STAPLE | ITKVoting | MajorityVoting | SIMPLE
-output OUTPUT The output file to write the resultsExample:
# continue from previous shell
python fusion_run \
-inputs /path/to/seg_algo_1.nii.gz,/path/to/seg_algo_2.nii.gz,/path/to/seg_algo_3.nii.gz \
-classes 0,1,2,4 \
-method STAPLE \
-output /path/to/seg_fusion.nii.gz# assuming virtual environment containing LabelFusion is activated
import SimpleITK as sitk
from LabelFusion.wrapper import fuse_images
label_to_fuse_0 = '/path/to/image_0.nii.gz'
label_to_fuse_1 = '/path/to/image_1.nii.gz'
images_to_fuse = []
images_to_fuse.append(sitk.ReadImage(label_to_fuse_0, sitk.sitkUInt8))
images_to_fuse.append(sitk.ReadImage(label_to_fuse_1, sitk.sitkUInt8))
fused_staple = fuse_images(images_to_fuse, 'staple') # class_list is not needed for staple/itkvoting
sitk.WriteImage(fused_staple, '/path/to/output_staple.nii.gz')
fused_simple = fuse_images(images_to_fuse, 'simple', class_list=[0,1,2,4])
sitk.WriteImage(fused_simple, '/path/to/output_simple.nii.gz')This repo has continuous integration enbabled via Azure DevOps for the following operating systems:
- Windows
- Ubuntu
- macOS
And for the following python versions:
- 3.6
- 3.7
- 3.8