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pyfMRIqc: a software package for raw fMRI data quality assurance

Williams, B. ORCID: and Lindner, M. (2020) pyfMRIqc: a software package for raw fMRI data quality assurance. Journal of Open Research Software, 8 (1). 23. ISSN 2049-9647

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To link to this item DOI: 10.5334/jors.280


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 ( 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.

Item Type:Article
Divisions:Interdisciplinary Research Centres (IDRCs) > Centre for Integrative Neuroscience and Neurodynamics (CINN)
Life Sciences > School of Psychology and Clinical Language Sciences > Neuroscience
ID Code:93457
Publisher:Ubiquity Press


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