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The LONI Pipeline workflow application gives users the necessary technology to describe their executables in a graphical interface (i.e. create a module). Pipeline allows users to connect their modules, creating complex analyses without the need for complex code in a scripting language. Pipeline streamlines the management of intermediate data in a script by passing data between programs automatically, eliminating the need to manage these transitions manually. Once you have created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. This helps with the maintenance and management of your modules.


The LONI Pipeline offers a host of features that enhance and enrich neuroimaging research. Read more >

Who Uses Pipeline?

A distributed LONI Pipeline client-server infrastructure is in use at the following institutions. Please contact us if you would like to get your organization on this list.

University of California,
Los Angeles

University of California, Irvine

Cincinnati Children’s Hospital

Emory University

University of Pittsburgh

University of Southern California

IRCCS Centro San Giovanni
di Dio – FBF

Australian National University

University of California,
San Francisco

Stanford University

California Institute of Technology

University of Pennsylvania

Northwestern University

University of Cincinnati

University of Illinois at Chicago

Ohio State University

Washington University
in St. Louis

University of Texas at Austin

University of Texas Health Science Center at San Antonio

St. Jude Children’s
Research Hospital

University of London

Queensland Institute of
Medical Research

McGill University


National Institutes of Health

Biomedical Informatics
Research Network

National Non-Human Primate
Research Centers

Johns Hopkins University

University of Wisconsin–Madison

Pennsylvania State University

Brigham and Women’s Hospital

Harvard University

University of Chicago

Frederick National Laboratory for Cancer Research

University of Michigan

Grid Monitor

Pipeline has a designated server called Cranium. You can follow the usage statistics and filter by job count, CPU hours or client connections for individual packages or all tools combined. Learn more >

LONI Cranium Library

The LONI Cranium Library Navigator offers Pipeline workflows, modules, data online with ability to view and/or run directly from the web using Pipeline Web Start.

Example Workflows

Browse an archive of workflows on our Twiki collaborative space.