University of Oulu

Huotari, N., Raitamaa, L., Helakari, H., Kananen, J., Raatikainen, V., Rasila, A., … Korhonen, V. O. (2019). Sampling Rate Effects on Resting State fMRI Metrics. Frontiers in Neuroscience, 13.

Sampling rate effects on resting state fMRI metrics

Saved in:
Author: Huotari, Niko1,2; Raitamaa, Lauri1,2; Helakari, Heta1,2;
Organizations: 1Oulu Functional NeuroImaging Group, Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland
2Department of Diagnostic Radiology, Medical Research Center, Oulu University Hospital, Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 4.2 MB)
Persistent link:
Language: English
Published: Frontiers Media, 2019
Publish Date: 2019-10-24


Low image sampling rates used in resting state functional magnetic resonance imaging (rs-fMRI) may cause aliasing of the cardiorespiratory pulsations over the very low frequency (VLF) BOLD signal fluctuations which reflects to functional connectivity (FC). In this study, we examine the effect of sampling rate on currently used rs-fMRI FC metrics. Ultra-fast fMRI magnetic resonance encephalography (MREG) data, sampled with TR 0.1 s, was downsampled to different subsampled repetition times (sTR, range 0.3–3 s) for comparisons. Echo planar k-space sampling (TR 2.15 s) and interleaved slice collection schemes were also compared against the 3D single shot trajectory at 2.2 s sTR. The quantified connectivity metrics included stationary spatial, time, and frequency domains, as well as dynamic analyses. Time domain methods included analyses of seed-based functional connectivity, regional homogeneity (ReHo), coefficient of variation, and spatial domain group level probabilistic independent component analysis (ICA). In frequency domain analyses, we examined fractional and amplitude of low frequency fluctuations. Aliasing effects were spatially and spectrally analyzed by comparing VLF (0.01–0.1 Hz), respiratory (0.12–0.35 Hz) and cardiac power (0.9–1.3 Hz) FFT maps at different sTRs. Quasi-periodic pattern (QPP) of VLF events were analyzed for effects on dynamic FC methods. The results in conventional time and spatial domain analyses remained virtually unchanged by the different sampling rates. In frequency domain, the aliasing occurred mainly in higher sTR (1–2 s) where cardiac power aliases over respiratory power. The VLF power maps suffered minimally from increasing sTRs. Interleaved data reconstruction induced lower ReHo compared to 3D sampling (p < 0.001). Gradient recalled echo-planar imaging (EPI BOLD) data produced both better and worse metrics. In QPP analyses, the repeatability of the VLF pulse detection becomes linearly reduced with increasing sTR. In conclusion, the conventional resting state metrics (e.g., FC, ICA) were not markedly affected by different TRs (0.1–3 s). However, cardiorespiratory signals showed strongest aliasing in central brain regions in sTR 1–2 s. Pulsatile QPP and other dynamic analyses benefit linearly from short TR scanning.

see all

Series: Frontiers in neuroscience
ISSN: 1662-4548
ISSN-E: 1662-453X
ISSN-L: 1662-4548
Volume: 13
Article number: 279
DOI: 10.3389/fnins.2019.00279
Type of Publication: A1 Journal article – refereed
Field of Science: 3126 Surgery, anesthesiology, intensive care, radiology
Funding: This work was supported by Jane and Aatos Erkko Foundation grant (VKi), Academy of Finland and Aivosäätiö TERVA grant 314497 (VKi), Academy of Finland Grants 123772 & 275342 (VKi), The SalWe Research Program for Mind and Body (Tekes—the Finnish Funding Agency for Technology and Innovation, Grant No. 1104/10) (VKi), Finnish Medical Foundation (VKi, TT), Finnish Neurological Foundation, KEVO grants from Oulu University Hospital (VKi), Epilepsy Research Foundation (JaK), Finnish Cultural Foundation, North Ostrobothnia Regional Fund (JaK), Orion Research Foundation sr (JaK, TT), Tauno Tönning Foundation (JaK) and Health and Biosciences Doctoral programme -grant (HH).
Academy of Finland Grant Number: 314497
Detailed Information: 314497 (Academy of Finland Funding decision)
123772 (Academy of Finland Funding decision)
Copyright information: © 2019 Huotari, Raitamaa, Helakari, Kananen, Raatikainen, Rasila, Tuovinen, Kantola, Borchardt, Kiviniemi and Korhonen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.