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DevelopingHCP / structural-pipeline

dHCP structural pipeline
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add a Dockerfile #3

Open jcupitt opened 6 years ago

jcupitt commented 6 years ago

It seems to work for me ... test with:

docker build \
    --build-arg VCS_REF=`git rev-parse --short HEAD` \
    -t <user>/structural-pipeline:latest .

Fetching the FSL key seems a little unreliable, I'm not sure why. If you get an error, try just running again.

see https://github.com/DevelopingHCP/structural-pipeline/issues/2

jcupitt commented 6 years ago

(Dockerfile shamelessly copied from MIRTK)

schuhschuh commented 6 years ago

Sweet! BTW I myself have no permissions to merge. Either wait for @amakropoulos's reply or get permissions from in-house if your part of BioMedIA/dHCP.

jcupitt commented 6 years ago

I added some notes to the README. It should probably use -v to attach the user's data files to the container for processing, I'll experiment.

jcupitt commented 6 years ago

It seems to be working well now. I'm going to merge to master on my fork, I'll leave this here.

The README has some notes -- tldr: build the pipeline to a docker image with:

# docker build -t <user>/structural-pipeline:latest .

Run the pipeline on the file sub-CC00183XX11_ses-60300_T2w.nii.gz in the subdirectory data of the current directory:

# docker run --rm -t -v $PWD/data:/data \
    <user>/structural-pipeline:latest \
    bash -c ". /etc/fsl/fsl.sh; \
        cd /usr/src/structural-pipeline; \
        ./dhcp-pipeline.sh subject1 session1 44 \
            -d /data -T2 /data/sub-CC00183XX11_ses-60300_T2w.nii.gz -t 8"

I'll try and get OpenMOLE using this next.