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Adding singularity commands in the example demo

Open armaneshaghi opened this issue 5 years ago • 1 comments

I wonder whether you could add singularity commands for quick demonstration in the Usage section. Currently it only has information for docker and command line.

armaneshaghi avatar Feb 12 '20 17:02 armaneshaghi

you can use the singularity equivalent of the docker command.

to get the singularity image: singularity pull docker://kaczmarj/nobrainer:latest-gpu

an example of running the nobrainer command line interface with singularity:

singularity run --nv --bind $PWD:/data SINGULARITY_IMAGE \
  predict \
    --model=/models/brain-extraction-unet-128iso-model.h5 \
    --verbose \
    /data/T1w.nii.gz \
    /data/brainmask.nii.gz

kaczmarj avatar Feb 12 '20 22:02 kaczmarj