LabelFusion

This repo contains implementation of various label fusion approaches that can be used to fuse multiple labels.

Installation

Default

conda create -n venv_labelFusion python=3.12 -y
conda activate venv_labelFusion
pip install LabelFusion

For Development

# fork to your own repo
git clone ${yourFork_labelFusion_repo_link}cd LabelFusion
conda create -p ./venv python=3.12 -y
conda activate ./venv
pip install -e .# develop, push# initiate pull request

Available fusion methods:

• 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

Usage

Command-Line interface

# 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 '0,1,2,3' - 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 results

Example:

# continue from previous shell
python fusion_run \
-inputs /path/to/seg_algo_0.nii.gz,/path/to/seg_algo_1.nii.gz,/path/to/seg_algo_2.nii.gz \
-classes 0,1,2,3 \
-method STAPLE \
-output /path/to/seg_fusion.nii.gz

Python interface

# assuming virtual environment containing LabelFusion is activatedimportSimpleITKassitkfromLabelFusion.wrapperimportfuse_imageslabel_to_fuse_0='/path/to/seg_algo_0.nii.gz'label_to_fuse_1='/path/to/seg_algo_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/itkvotingsitk.WriteImage(fused_staple, '/path/to/output_staple.nii.gz')
fused_simple=fuse_images(images_to_fuse, 'simple', class_list=[0,1,2,3])
sitk.WriteImage(fused_simple, '/path/to/output_simple.nii.gz')

Testing

This repo has continuous integration enabled via GitHub Actions for the following operating systems:

• Windows
• Ubuntu
• macOS

And for the following python versions:

• 3.9
• 3.10
• 3.11
• 3.12