Elimination of k-space spikes in fMRI data Xiaodong Zhang, Pierre-Francois Van De Moortele, Josef Pfeuffer, Xiaoping Hu* Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA Abstract The subtle signal changes in functional magnetic resonance imaging (fMRI) can be easily overwhelmed by noise of various origins. Spikes in the collected fMRI raw data often arise from high-duty usage of the scanner hardware and can introduce significant noise in the image and thereby in the image time series. Consequently, the spikes will corrupt the functional data and degrade the result of functional mapping. In this work, a simple method based on processing the time course of the k-space data are introduced and implemented to remove the spikes in the acquired data. Application of the method to experimental data shows that the methods are robust and effective for eliminating of spike-related noise in fMRI time series. © 2001 Elsevier Science Inc. All rights reserved. Keywords: fMRI; EPI; Spike noise removal; K-space 1. Introduction Despite its routine use in studying brain function, func- tional magnetic resonance imaging (fMRI) based on the blood oxygenation level dependent or BOLD contrast is still limited by a number of factors. In particular, activation induced signal changes are often small and may be over- whelmed by artifactual signal changes caused by gross body movements, physiological fluctuation, and system instabil- ities [1,2]. These artifacts have been known to degrade the fMRI data and hamper the detection of activation induced BOLD response. A number of methods are available for their correction [1,3,4]. Recent advances in fMRI have moved it to the domain of high spatial (1 mm) and temporal resolutions (100 ms), extending its utility in neuroscience. However, due to im- perfections in gradient coil, RF hardware, or other hardware components, noise spikes may appear in the acquired k- space data, especially when strong gradients are employed at a high duty cycle. The contribution of a single spike is a sinusoid oscillation in the image domain. Spikes appearing randomly in the k-space introduce complicated noises in the im- age domain, degrading the signal-to-noise ratio of the fMRI data. In general, spikes appear randomly in the k-space. Fur- thermore, their occurrence in time is also random. A number of these sporadic spikes in the k-space data for each image add a complicated pattern to the original image and their random occurrence in time leads to detrimental spike-like fluctuations in the time series. While it is possible to reduce this kind of fluctuations with a low-pass filter or other methods [5,6], filtering is insufficient for intense spikes because their energy spreads over a wide range of temporal frequency. In addition, filtering may introduce unwanted smoothing of the time course. An algorithm for removing spikes in the k-space data were recently introduced and applied to fMRI [7]. For each image, spikes are detected based on Hermitian symmetry and removed by replacing the corrupted k-space data with the value predicted by Hermitian symmetry [8]. For an fMRI time series, the procedure is carried out image by image. While this algorithm worked reasonably well, it cannot be applied to partial Fourier data and does not work robustly near the center of the k-space where the spike amplitude is comparable to the magnitude of the actual k-space signal. In this note, we describe a method for removing spikes in fMRI data based on the analysis of the k-space time series. Results on experimental data were obtained and demonstrated that the method worked effectively and robustly for fMRI. 2. Methods Examination of the EPI raw data reveals that spikes appear randomly in the k-space and time. In order to elim- * Corresponding author. Tel.: +1-612-626-7411; fax: +1-612-626-2004. E-mail address: xiaoping@cmrr.umn.edu (X. Hu). Work supported by the National Institutes of Health (Grants R01MH55346 and RR07809). Magnetic Resonance Imaging 19 (2001) 1037–1041 0730-725X/01/$ – see front matter © 2001 Elsevier Science Inc. All rights reserved. PII: S0730-725X(01)00428-3