Open Recon

These instructions were tested on GitHub Codespaces, and we recommend this as a starting point.

For a local setup you need Docker (https://www.docker.com/), Python3 and you need to install neurodocker and add it to your path:

python -m pip install neurodocker
#the path depends on your local setup
export PATH=$PATH:~/.local/lib/python3.12/site-packages/bin
export PATH=$PATH:~/.local/bin

1) add the installation of the Python MRD server to any recipe in https://github.com/neurodesk/neurocontainers

Make sure to adjust invertcontrast.py to your pipeline needs (or replace/rename other files from the Python MRD server:

- include: macros/openrecon/neurodocker.yaml

here is an example: https://github.com/NeuroDesk/neurocontainers/tree/main/recipes/openreconexample

Then build the recipe:

sf-login openreconexample --architecture x86_64

2) test the tool inside the container on its own first and then test through MRD server

convert dicom data to mrd test data:

cd /opt/code/python-ismrmrd-server
python3 dicom2mrd.py -o input_data.h5 PATH_TO_YOUR_DICOM_FILES

start server and client and test application:

python3 /opt/code/python-ismrmrd-server/main.py -v -r -H=0.0.0.0 -p=9002 -s -S=/tmp/share/saved_data &
# wait until you see Serving ... and the press ENTER
python3 /opt/code/python-ismrmrd-server/client.py -G dataset -o openrecon_output.h5 input_data.h5

3) submit the container to the https://github.com/NeuroDesk/openrecon/ repository

here is an example: https://github.com/NeuroDesk/openrecon/tree/main/recipes/openreconexample