FSL - FMRIB Software Library

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data, created by the Analysis Group, FMRIB, Oxford, UK. See https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL for more information.

Basic concept (for oSPARC UI Services)

An osparc-ui module consists of two services, a web proxy web and the actual application app. The web service acts only as a proxy for integration into the osparc platform. The app service consists of the X11 based GUI application that should be accessible via the osparc iframe and some additional supporting programs:

• supervisord: to control the processes in the container
• xtigervnc: VNC client/server application with embedded X-server
• novnc: opensource javascript vnc client
• openbox: Minimal window manager

Usage

Build the module:

$ make build

To run locally at and visit http://127.0.0.1:28080

make run-local

To publish in local throw-away registry:

make publish-local

Test the application with some actual data

In a local deployment, you should be able to use the FSL GUI. You can try out different commands (by clicking on the respective button). For instance, you can try out the BET tools with the input file in (validation/inputs/).

Workflow

1. The application should be installed via modification of the Dockerfile in fsl/app
2. The [program:app] section in supervisord.conf in fsl/app/config needs to be modified to accomodate to the correct command line for the program.

Versioning

• To update service version use one of the commands make version-*

CI/CD Integration

A template ci config file is created infsl/.github/workflows/check-image.yml. Then CI are monitored by the publisher repo on GitLab that takes care of publishing a new version.