brainlife/ants repository overview

⁠ants-docker

A Dockerfile for ANTs 2.3.1 (Avants et al., 2011) with:

• HCP Pipelines (Glasser et al., 2013) cloned at /opt/HCPpipelines
• MNI152 templates (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009⁠) downloaded into /atlas

⁠Maintainers

Gabriele Amorosino ([email protected]⁠)

⁠Run (Docker)

docker run --rm -it \
  brainlife/ants-docker:2.3.1 \
  <your_command>

⁠Run (Singularity)

⁠From your local Docker image

singularity build ants-2.3.1.sif \
  docker-daemon://brainlife/ants-docker:2.3.1

singularity exec \
  --bind $(pwd):/workspace \
  ants-2.3.1.sif \
  <your_command>

⁠Directly from Docker Hub

singularity exec \
  docker://brainlife/ants-docker:2.3.1 \
  <your_command>

⁠Contents

• ANTs 2.3.1 installed in a Conda env named ants-2.3.1
• HCP Pipelines repo: /opt/HCPpipelines
• MNI152 templates unpacked under /atlas

⁠Reference

• Avants, B. B., Tustison, N. J., Song, G., Cook, P. A., Klein, A., & Gee, J. C. (2011). A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage, 54(3), 2033-2044.
• Glasser, M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B., Andersson, J. L., ... & Wu-Minn HCP Consortium. (2013). The minimal preprocessing pipelines for the Human Connectome Project. Neuroimage, 80, 105-124.