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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:

  • set up project-based workflows with project specific and experiment specific parameters,
  • track a pipeline and send email notifications, and
  • capture provenance information as the pipeline executes.

In order to run a pipeline, two things need to happen:

Running Pipelines 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.  

  • Click Build within the Actions box at the right. 
  • Select the pipelines to run from the pop-up window

  • Click Submit
  • A new window will open with the message

Your pipeline is now running! 

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