Docker Usage

OncoPrep is available as a Docker image with all neuroimaging dependencies (ANTs, FSL, dcm2niix) pre-installed.

Pull the image

docker pull nko11/oncoprep:latest

Basic preprocessing

docker run --platform linux/amd64 --rm \
  -v /path/to/bids:/data/bids:ro \
  -v /path/to/output:/data/output \
  -v /path/to/work:/data/work \
  nko11/oncoprep:latest \
  /data/bids /data/output participant \
  --participant-label sub-001

With segmentation

Segmentation launches Docker containers for each model, so the host Docker socket must be mounted:

docker run --platform linux/amd64 --rm \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v /path/to/bids:/data/bids:ro \
  -v /path/to/output:/data/output \
  -v /path/to/work:/data/work \
  nko11/oncoprep:latest \
  /data/bids /data/output participant \
  --participant-label sub-001 --run-segmentation --default-seg

GPU ensemble mode (Linux)

docker run --rm --gpus all \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v /path/to/bids:/data/bids:ro \
  -v /path/to/output:/data/output \
  -v /path/to/work:/data/work \
  nko11/oncoprep:latest \
  /data/bids /data/output participant \
  --participant-label sub-001 --run-segmentation

DICOM conversion

docker run --platform linux/amd64 --rm \
  -v /path/to/dicoms:/data/dicom:ro \
  -v /path/to/bids:/data/bids \
  --entrypoint oncoprep-convert \
  nko11/oncoprep:latest \
  /data/dicom /data/bids --subject 001

Build from source

docker build --platform linux/amd64 -t oncoprep:latest .

Warning

The image targets linux/amd64. On Apple Silicon Macs, Docker Desktop uses Rosetta emulation automatically, but ANTs binaries may hit Illegal instruction errors. Use the native pip install for local development on ARM Macs.