Journal
FRONTIERS IN NEUROINFORMATICS
Volume 13, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fninf.2019.00005
Keywords
functional magnetic resonance imaging; data preprocessing; volume- and surface-based preprocessing; fully automated software; fusion of existing software
Funding
- Institute for Basic Science [IBS-R015-D1]
- NRF (National Research Foundation of Korea) [NRF-2016H1A2A1907833, NRF-2016R1A2B4008545]
- Ministry of Science and ICT of Korea under the ITRC program [IITP-2018-2018-0-01798]
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The preprocessing of functional magnetic resonance imaging (fMRI) data is necessary to remove unwanted artifacts and transform the data into a standard format. There are several neuroimaging data processing tools that are widely used, such as SPM, AFNI, FSL, FreeSurfer, Workbench, and fMRlPrep. Different data preprocessing pipelines yield differing results, which might reduce the reproducibility of neuroimaging studies. Here, we developed a preprocessing pipeline for T1 -weighted structural MRI and fMRI data by combining components of well-known software packages to fully incorporate recent developments in MRI preprocessing into a single coherent software package. The developed software, called FuNP (Fusion of Neuroimaging Preprocessing) pipelines, is fully automatic and provides both volume- and surface-based preprocessing pipelines with a user-friendly graphical interface. The reliability of the software was assessed by comparing resting-state networks (RSNs) obtained using FuNP with pre-defined RSNs using open research data (n = 90). The obtained RSNs were well-matched with the pre-defined RSNs, suggesting that the pipelines in FuNP are reliable. In addition, image quality metrics (IQMs) were calculated from the results of three different software packages (i.e., FuNP, FSL, and fMRlPrep) to compare the quality of the preprocessed data. We found that our FuNP outperformed other software in terms of temporal characteristics and artifacts removal. We validated our pipeline with independent local data (n = 28) in terms of IQMs. The IQMs of our local data were similar to those obtained from the open research data. The codes for FuNP are available online to help researchers.
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