Linda BIDS App

[chrisgorgo]

@stnava suggested it might be beneficial to build a BIDS App for the LINDA pipeline

This is as simple as writing a short script parsing input BIDS dataset and putting everything in a docker container. The big advantage of this approach is that it would allow us to host this (for free) on http://OpenNeuro.org. This new platform lets users run long and computationally expensive workflows in the cloud. It's free and will remain this way - the goal is to get people to share more data.

This approach have benefits for you - it makes your software more accessible (and we make sure appropriate credit is given to each app) and easier to debug (since you can interrogate all files and logs online). Building a BIDS App is fairly easy (more info here and an example here). I feel that two most sensible ANTs workflows would be: cortical thickness calculation and study specific template building.

More resources:

• http://bids-apps.neuroimaging.io
• http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209
• https://github.com/BIDS-Apps/example

Let me know if you are interested - I would be happy to help.

[dorianps]

Chris, sorry for missing this thread before. I will look into this and see what's the best approach. Probably is better to have LESYMAP in there, which has more mature code. LINDA is a bit too primitive on the way it's written and I am not maintaining it much.

One thing I have been trying to achieve is some sort of web interface (ShinyApp) with ANTsR in the background. If that can be achieved in OpenNeuro, it would be great.

[chrisgorgo]

I opened an issue on LESYMAP for clarity. The tool looks very cool and a great match!

OpenNeuro provides basic UI for apps to map user inputs. This includes string inputs, checkboxes, radio buttons, dropdown lists, and file uploads. I hope this helps!