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LONI Pipeline Processing Environment

A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve 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. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.

URL: http://www.loni.usc.edu/Software/Pipeline

Resource ID: nif-0000-00322     Resource Type: Resource     Version: Latest Version


workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing

Additional Resource Types

Workflow Software


LONI Software License




LONI Pipeline


LONI Pipeline Environment

Parent Organization

Funding Information

NIH, P41 RR013642, R01 MH71940, U54 RR021813

Listed By

NITRC, Biositemaps

Old URLs


Original Submitter


Version Status


Submitted On

12:00am September 21, 2010

Originated From


Changes from Previous Version

  • Description was changed
  • Additional Resource Types was changed

Version 2

Created 2 weeks ago by Christie Wang

Version 1

Created 5 years ago by Anonymous

The LONI Pipeline Processing Environment.

  • Rex DE
  • Neuroimage
  • 2003 25

The analysis of raw data in neuroimaging has become a computationally entrenched process with many intricate steps run on increasingly larger datasets. Many software packages exist that provide either complete analyses or specific steps in an analysis. These packages often possess diverse input and output requirements, utilize different file formats, run in particular environments, and have limited abilities with certain types of data. The combination of these packages to achieve more sensitive and accurate results has become a common tactic in brain mapping studies but requires much work to ensure valid interoperation between programs. The handling, organization, and storage of intermediate data can prove difficult as well. The LONI Pipeline Processing Environment is a simple, efficient, and distributed computing solution to these problems enabling software inclusion from different laboratories in different environments. It is used here to derive a T1-weighted MRI atlas of the human brain from 452 normal young adult subjects with fully automated processing. The LONI Pipeline Processing Environment's parallel processing efficiency using an integrated client/server dataflow model was 80.9% when running the atlas generation pipeline from a PC client (Acer TravelMate 340T) on 48 dedicated server processors (Silicon Graphics Inc. Origin 3000). The environment was 97.5% efficient when the same analysis was run on eight dedicated processors.