Literature DB >> 28919661

DAX - The Next Generation: Towards One Million Processes on Commodity Hardware.

Stephen M Damon1, Brian D Boyd2, Andrew J Plassard1, Warren Taylor2, Bennett A Landman1,2.   

Abstract

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with >100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner.

Entities:  

Keywords:  High Performance Computing; Pipelines; XNAT

Year:  2017        PMID: 28919661      PMCID: PMC5596878          DOI: 10.1117/12.2254371

Source DB:  PubMed          Journal:  Proc SPIE Int Soc Opt Eng        ISSN: 0277-786X


  6 in total

1.  The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

Authors:  Blake C Lucas; John A Bogovic; Aaron Carass; Pierre-Louis Bazin; Jerry L Prince; Dzung L Pham; Bennett A Landman
Journal:  Neuroinformatics       Date:  2010-03

2.  Next Generation of the Java Image Science Toolkit (JIST): Visualization and Validation.

Authors:  Bo Li; Frederick Bryan; Bennett A Landman
Journal:  Insight J       Date:  2012-08-15

Review 3.  FreeSurfer.

Authors:  Bruce Fischl
Journal:  Neuroimage       Date:  2012-01-10       Impact factor: 6.556

4.  Vanderbilt University Institute of Imaging Science Center for Computational Imaging XNAT: A multimodal data archive and processing environment.

Authors:  Robert L Harrigan; Benjamin C Yvernault; Brian D Boyd; Stephen M Damon; Kyla David Gibney; Benjamin N Conrad; Nicholas S Phillips; Baxter P Rogers; Yurui Gao; Bennett A Landman
Journal:  Neuroimage       Date:  2015-05-16       Impact factor: 6.556

5.  Performance Management of High Performance Computing for Medical Image Processing in Amazon Web Services.

Authors:  Shunxing Bao; Stephen M Damon; Bennett A Landman; Aniruddha Gokhale
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2016-03-25

Review 6.  SPM: a history.

Authors:  John Ashburner
Journal:  Neuroimage       Date:  2011-10-17       Impact factor: 6.556

  6 in total
  2 in total

Review 1.  Towards Portable Large-Scale Image Processing with High-Performance Computing.

Authors:  Yuankai Huo; Justin Blaber; Stephen M Damon; Brian D Boyd; Shunxing Bao; Prasanna Parvathaneni; Camilo Bermudez Noguera; Shikha Chaganti; Vishwesh Nath; Jasmine M Greer; Ilwoo Lyu; William R French; Allen T Newton; Baxter P Rogers; Bennett A Landman
Journal:  J Digit Imaging       Date:  2018-06       Impact factor: 4.056

2.  Application of Machine Learning to Automated Analysis of Cerebral Edema in Large Cohorts of Ischemic Stroke Patients.

Authors:  Rajat Dhar; Yasheng Chen; Hongyu An; Jin-Moo Lee
Journal:  Front Neurol       Date:  2018-08-21       Impact factor: 4.003

  2 in total

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