PyfMRIqc: A Software Package for Raw fMRI Data Quality Assurance. Issue 1 (7th October 2020)

• Record Type: Journal Article
• Authors: Williams, Brendan; Lindner, Michael
• Is Part Of: Journal of open research software. Volume 8:Issue 1(2020)
• Publication Date: 2020-10-07
• Subjects: neuroscience -- neuroimaging -- fMRI -- Python -- quality control -- artefacts; Computer software -- Reusability -- Periodicals; Open source software -- Periodicals; 005
• DOI: 10.5334/jors.280
• Languages: English
• ISSNs: 2049-9647

Abstract

PyfMRIqc is a tool for checking the quality of raw functional magnetic resonance imaging (fMRI) data. pyfMRIqc produces a range of output files which can be used to identify fMRI data quality issues such as artefacts, motion, signal loss etc. This tool creates a number of 3D and 4D NIFTI files that can be used for in depth quality assurance. Additionally, 2D images are created for each NIFTI file for a quick overview. These images and other information (e.g. about signal-to-noise ratio, scan parameters, etc.) are combined in a user-friendly HTML output file. pyfMRIqc is written entirely in Python and is available under a GNU GPL3 license on GitHub (https://drmichaellindner.github.io/pyfMRIqc/ ). pyfMRIqc can be used from the command line and therefore can be included as part of a processing pipeline or used to quality-check a series of datasets using batch scripting. The quality assurance of a single dataset can also be performed via dialog boxes.