jhuguetn/samseg repository overview

⁠SAMSEG Docker image

Lightweight Docker image for reproducible FreeSurfer SAMSEG execution.

• FreeSurfer SAMSEG: https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg⁠

Find the image in Docker Hub here⁠.

⁠Components

• Ubuntu 20.04
• FreeSurfer 7.4.1
• SAMSEG (bundled with the official FreeSurfer 7.4.1 image)

The image is derived from the official freesurfer/freesurfer:7.4.1 Docker image while excluding unrelated FreeSurfer components.

⁠Usage

docker run --rm -it jhuguetn/samseg:7.4.1 --help

Example T1w segmentation:

mkdir -p ./data/out

docker run --rm -it \
  -v $(pwd)/data:/data \
  jhuguetn/samseg:7.4.1 \
  --input /data/T1w.nii.gz \
  --output /data/out \
  --threads 4

⁠License

FreeSurfer, SAMSEG and associated resources included in the resulting image remain governed by their respective upstream license terms.

⁠Notes

• Derived from FreeSurfer 7.4.1⁠
• Intended for reproducible research workflows and as a base image for workflow-specific containers

⁠Credits

Jordi Huguet (BarcelonaBeta Brain Research Center⁠)