How to share reproducible FSL analysis pipelines
The Open Analysis Working Group has worked with researchers to capture details of the magnetic resonance imaging (MRI) tools that they use in data processing. WIN is the developmental home of the popular FMRIB Software Library (FSL) MRI analysis package, which has been free to all users since its inception. FSL this is the tool of choice for most WIN researchers. The Working Group has devised a processes which researchers can slot into their normal FSL usage to ensure their analysis is reproducible and can be easily shared with others.
International community data standards - specifically the Brain Imaging Data Structure (BIDS) - have been employed to ensure that shared pipelines are compatible with tools developed elsewhere. This working group is also committed to actively engaging with the future development of BIDS, to ensure lifetime compatibility between FSL and the wide data standards.
Another large focus of this working group is developing programming literacy among WIN members, to support users in creating robust code to run their analysis. Significant efforts have been made to update the FSL training material, which is now available for free both internally and externally, and has been updated to include basic training in Unix command line access. The FSL course is being run remotely and at reduced registration rates for the first time in 2020, for improved accessibility and inclusivity.
THIS TOOL IS CURRENTLY IN DEVELOPMENT. PLEASE REFER TO THE INFORMATION BELOW TO UNDERSTAND THE AIM AND AMBITION OF THIS PROJECT. THE “HOW TO” GUIDE WILL BE BUILT BY THE COMMUNITY AND TOOL DEVELOPERS IN THE COMING MONTHS.
WIN members will be encouraged to develop their analysis pipelines into standalone scripts and store these on the WIN GitLab instance. We will support our members in using git to version control their code, and employ best practice in ensuring their pipelines are robust and accurate. Find out more about using GitLab
Versions of analysis code can be assigned a digital object identified (DOI) using Zenodo by uploading them from GitLab. Once a DOI has been created, your analysis code becomes a citable object which you can add to your list of research outputs. Find out how to create a doi for your repository.
Alongside your analysis code, WIN members will be supported in implementing a “wrapper” script which can:
- access data stored on the WIN Open Data servers;
- access your GitLab code repository;
- pull a stable version of the FSL analysis package in a Singularity container;
- Run the accessed data using the supplied code and the given version of FSL via the container on a high performance cluster.
The benefit of the above comes from version control of the singularity container and that it encompasses a complete computational environment, such that it can be run on any operating system without concern over dependencies of versions of packages, making the analysis highly reproducible.
External users will be able to access the shared code and singularity containers, along with data when this is shared openly, and repeat the analysis to probe the results. External users will also be able to modify shared analysis code to suit there own needs, where this is shared with a permissive license.
Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our documentation hacks
You are free to include whatever material you wish in your repository. We have created this guide on what to include to list some of the pages and sections which may be beneficial for readers. See also our guide on how to license your material.
We recommend using zenodo to create a doi for your material. See see the creating a doi page for instructions.
We are grateful to the following WIN members for their contributions to developing the Open Analysis tools