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© 2016. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

The contribution of this paper is to describe how we can program neuroimaging workflow using Make, a software development tool designed for describing how to build executables from source files. We show that we can achieve many of the features of more sophisticated neuroimaging pipeline systems, including reproducibility, parallelization, fault tolerance, and quality assurance reports. We suggest that Make represents a large step towards these features with only a modest increase in programming demands over shell scripts. This approach reduces the technical skill and time required to write, debug, and maintain neuroimaging workflows in a dynamic environment, where pipelines are often modified to accommodate new best practices or to study the effect of alternative preprocessing steps, and where the underlying packages change frequently. This paper has a comprehensive accompanying manual with lab practicals and examples (see Supplemental Materials) and all data, scripts and makefiles necessary to run the practicals and examples are available in the “makepipelines” project at NITRC.

Details

Title
Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance
Author
Askren, Mary K; McAllister-Day, Trevor K; Koh, Natalie; Mestre, Zoé; Dines, Jennifer N; Korman, Benjamin A; Melhorn, Susan J; Peterson, Daniel J; Peverill, Matthew; Qin, Xiaoyan; Rane, Swati D; Reilly, Melissa A; Reiter, Maya A; Sambrook, Kelly A; Woelfer, Karl A; Grabowski, Thomas J; Madhyastha, Tara M
Section
Technology Report ARTICLE
Publication year
2016
Publication date
Feb 2, 2016
Publisher
Frontiers Research Foundation
e-ISSN
16625196
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2295434228
Copyright
© 2016. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.