This documentation is for XNAT versions 1.6.0 - 1.6.5. You can find the latest documentation for XNAT 1.7 at https://xnat.org/documentation
Pipelines in XNAT are powerful mini-applications that can be run on your project data, to aid in complex processing or leverage the power of large computing clusters. Some pipeline-enabled workflows are carried out automatically without any human intervention, like auto-QC'ing images as they are added to your project archive. Others require a person to do manual steps, such as drawing a region of interest.
When pipelines are integrated into your project, you can:
As the project owner, you can add any pipeline that is active in XNAT. This is done from the project report page, under the PIPELINES tab. Here is a step-by-step walkthrough.
You can then close the popup window, and your pipeline will be active on your project.
For the most part, pipelines do not directly modify your experiment data; instead, they add additional data to your project as Assessors. (Related: Understanding the XNAT Data Model)
To run a pipeline, you must first have installed a pipeline, of course. Then, navigate to the experiment report page (for example, an MR Session page) in XNAT.
Your pipeline is now running!