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CONTRIBUTING.md

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Contributing

If you want to contribute to LAYNII and make it better, your help is very welcome.

Opening an issue

  • Please post your questions, bug reports and feature requests to our issues page.
  • When reporting a bug, please specify your system and a complete copy of the error message that you are getting.

Making a pull request

  • Create a personal fork of the project on Github.
  • Clone the fork on your local machine.
  • Create a new branch to work on. Branch from devel.
  • Implement/fix your feature, comment your code.
  • Follow the code style of the project.
  • Add or change the documentation as needed.
  • Push your branch to your fork on Github.
  • From your fork open a pull request in the correct branch. Target devel branch of the original Segmentator repository.

Note: Please write your commit messages in the present tense. Your commit message should describe what the commit, when applied, does to the code – not what you did to the code.

Docker

The Dockerfile is created using neurodocker.

Preferably modify the recipe in the Makefile than the Dockerfile directly.

Build the Dockerfile:

make Dockerfile

Building the image

make docker_build

Smoke test of the image:

INPUT_DIR=${PWD}/test_data

mkdir ${PWD}/output
OUTPUT_DIR=${PWD}/output

docker run -it --rm \
           -v "${OUTPUT_DIR}":/output \
           -v "${INPUT_DIR}":/input \
           --user "$(id -u):$(id -g)" \
    laynii:latest \
        LN_BOCO \
        -Nulled "/input/lo_Nulled_intemp.nii" \
        -BOLD "/input/lo_BOLD_intemp.nii" \
        -trialBOCO 40 -shift \
        -output /output/lo_BOLD

# clean up after test
rm -rf output

This guideline is adapted from link