Journal Article

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Craddock, R. Cameron, Kiar, Gregory, Liem, Franziskus, Steele, Christopher J., Esteban, Oscar, Cohen, Alexander Li, Gorgolewski, Krzysztof J., Wang, Yida, Keshavan, Anisha, Flandin, Guillaume, Chakravarty, M. Mallar, Devenyi, Gabriel A., Ghosh, Satrajit S., Auer, Tibor, Bellec, Pierre, Quirion, Pierre-Olivier, Raamana, Pradeep Reddy, Strother, Stephen C., Alfaro-Almagro, Fidel, Guntupalli, J. Swaroop, Eklund, Anders, Smith, Robert E., Churchill, Nathan W., Raffelt, David, Yarkoni, Tal, Jenkinson, Mark, Varoquaux, Gaël, Capotă, Mihai, Poldrack, Russell A.

2017

Overview

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Abnormalities / Accessibility / Aging / Algorithms / Anatomy / Archiving / Automation / Bioengineering / Bioinformatics / Biology and Life Sciences / Biomedical engineering / Biophysics / Brain / Brain - anatomy & histology / Brain mapping / Brain research / Cerebellum / Children / Computational neuroscience / Computer and Information Sciences / Computer applications / Computer networks / Computer programs / Containers / Data acquisition / Data analysis / Data processing / Diagnostic imaging / Diffusion weighted imaging / Distributed processing / Engineering / Engineering and Technology / Functional magnetic resonance imaging / Health sciences / Heterogeneity / High resolution / Hippocampus / Hum / Humans / Image Interpretation, Computer-Assisted - methods / Image processing / Information processing / Information systems / Luteinizing hormone / Magnetic resonance imaging / Magnetic Resonance Imaging - methods / Medical imaging / Medical research / Medicine and Health Sciences / Mental disorders / Mental health / Neostriatum / Nervous system / Neuroimaging / Neuroimaging - methods / Neurological research / Neurology / Neurosciences / NMR / Noise / Nuclear magnetic resonance / Operating systems / Operations research / Packaging / Parallel processing / Probability theory / Psychiatry / Psychology / Radiology Information Systems - organization & administration / Reproducibility / Research and Analysis Methods / Resonance / Schizophrenia / Scientific software / Segmentation / Software / Software development / Software tools / Spring (season) / Technology / Technology application / Technology utilization / User-Computer Interface