SynthStrip WebGPU

This project is a work-in-progress port of the SynthStrip neural network based brain extraction tool to WebGPU.

Planned porting steps

• Export synthstrip model to onnx
• Use wonnx to run the onnx model through webgpu
• Port surfa.Volume, surfa.load_volumes, and surfa.stack for pre/post-processing
• Deploy a demo site that takes in a full NIfTI volume of the head, and outputs the brain extrected nifti volume

Usage

Configure python environment

python -m venv venv
source ./venv/bin/activate
pip install -r ./requirements.txt

Run command

python ./synth_clean.py -i ./test_t1.nii -o ./out.nii -m ./mask.nii -d ./sdt.nii