pyfMRIqc: A Software Package for Raw fMRI Data Quality Assurance

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.