Abstract
Subject-level independent component analysis (ICA) is a well-established and widely used approach in denoising of resting-state functional magnetic resonance imaging (fMRI) data. However, approaches such as ICA-FIX and ICA-AROMA require advanced setups and can be computationally intensive. Here, we aim to introduce a user-friendly, computationally lightweight toolbox for labeling independent signal and noise components, termed Alternative Labeling Tool (ALT). ALT uses two features that require manual tuning: proportion of an independent component’s spatial map located inside gray matter and positive skew of the power spectrum. ALT is tightly integrated with the commonly used FMRIB’s statistical library (FSL). Using the Open Access Series of Imaging Studies (OASIS-3) ageing dataset (n = 275), we found that ALT shows a high degree of inter-rater agreement with manual labeling (over 86% of true positives for both signal and noise components on average). In conclusion, ALT can be extended to small and large-scale datasets when the use of more complex tools such as ICA-FIX is not possible. ALT will thus allow for more widespread adoption of ICA-based denoising of resting-state fMRI data.
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Data used in the preparation of this article were obtained from the OASIS-3 database (https://www.oasis-brains.org/) and are freely available after registration. The code and the gray matter mask used freely available at https://github.com/peterzhukovsky/alt
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Funding
PZ was funded by a CIHR postdoctoral fellowship. GC was funded by Alzheimer Society postdoctoral fellowship grant. ANV received research funding from CIHR, NIH, and CAMH foundation. CH received research funding from CIHR, NIMH, and CAMH foundation.
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Manuscript writing: All authors.
Study Design: All authors.
Data Analysis: PZ.
Image Labeling: PZ, GC.
ALT development: PZ, GC.
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This work used open access data from the OASIS3 study. Ethical Approval for OASIS3 study was obtained from the relevant Review Ethical Board by the OASIS3 Principal Investigators: T. Benzinger, D. Marcus, J. Morris; NIH P50 AG00561, P30 NS09857781, P01 AG026276, P01 AG003991, R01 AG043434, UL1 TR000448, R01 EB009352. AV-45 doses were provided by Avid Radiopharmaceuticals, a wholly owned subsidiary of Eli Lilly. http://www.oasis-brains.org
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Zhukovsky, P., Coughlan, G., Dickie, E.W. et al. Alternative labeling tool: a minimal algorithm for denoising single-subject resting-state fMRI data with ICA-MELODIC. Brain Imaging and Behavior 16, 1823–1831 (2022). https://doi.org/10.1007/s11682-022-00650-9
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DOI: https://doi.org/10.1007/s11682-022-00650-9