An Automated Open-Source Workflow for Standards-Compliant Integration of Small Animal Magnetic Resonance Imaging Data
OPEN ACCESS
Loading...
Author / Producer
Date
2020-02
Publication Type
Journal Article
ETH Bibliography
yes
Citations
Altmetric
OPEN ACCESS
Data
Rights / License
Abstract
Large-scale research integration is contingent on seamless access to data in standardized formats. Standards enable researchers to understand external experiment structures, pool results, and apply homogeneous preprocessing and analysis workflows. Particularly, they facilitate these features without the need for numerous potentially confounding compatibility add-ons. In small animal magnetic resonance imaging, an overwhelming proportion of data is acquired via the ParaVision software of the Bruker Corporation. The original data structure is predominantly transparent, but fundamentally incompatible with modern pipelines. Additionally, it sources metadata from free-field operator input, which diverges strongly between laboratories and researchers. In this article we present an open-source workflow which automatically converts and reposits data from the ParaVision structure into the widely supported and openly documented Brain Imaging Data Structure (BIDS). Complementing this workflow we also present operator guidelines for appropriate ParaVision data input, and a programmatic walk-through detailing how preexisting scans with uninterpretable metadata records can easily be made compliant after the acquisition.
Permanent link
Publication status
published
External links
Editor
Book title
Journal / series
Volume
14
Pages / Article No.
5
Publisher
Frontiers Media
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
MRI/fMRI; small animal imaging; repositing; FOSS; Bruker; ParaVision; Python
Organisational unit
09474 - Yanik, Mehmet Fatih / Yanik, Mehmet Fatih
Notes
Funding
Related publications and datasets
Is new version of: https://doi.org/10.3929/ethz-b-000394461