Functional Brain Signal Processing: EEG & fMRI Lesson 12 Kaushik Majumdar Indian Statistical Institute Bangalore Center M.Tech. (CS), Semester III, Course B50

fMRI Noise Scanner noise. Thermal noise – heat generated in the coils will alter resistance and current flow, which will affect magnetization and will lead to randomly fluctuating noise in the image. Physiological noise – for example, ionic currents from different parts of the body will add noise to the image.

SNR in fMR Images If B 0 is high transverse magnetic field M 0 will have to be high, the SNR will be high. Voxel volume – the more it is the more protons are there inside, so the stronger the signal is. But point spread function (PSF) and Gibbs phenomenon makes it more complicated. Total time for imaging.

Point Spread Function and Gibb’s Phenomenon Buxton, 2009

T 2 * Time Effect Since, if acquisition time is increased the SNR will be improved. But we also have. So acquisition time is bounded above by T 2 * relaxation time.

fMRI Artifacts: Scanner Spikes Poldrack et al., 2011

Ghost Image Ghost images are associated with EPI and body movements. Buxton, 2009

Distortion Poldrack et al., 2011 Distortion happens due to magnetic inhomogeneity at the interface between tissue and air. It happens during EPI (left) acquisition. The above image is corrected (middle) by superposition with the T 1 weighted image (right).

Slice Timing Artifact Poldrack et al., 2011 Not very important and not done in most modern acquisition systems.

Slice Timing Correction Poldrack et al., 2011

Motion Artifacts Poldrack et al., 2011

Motion Correction Poldrack et al., 2011

Motion Correction (cont) Poldrack et al., 2011

Motion Artifact: Spin History Effect When the head moves, the protons that move into a voxel from the neighboring voxels have an excitation that is different from that expected by the scanner, and the reconstructed voxel will not accurately reflect the tissue in the voxel.

Heart Motion Artifact Buxton, 2009

Ionic Motion Artifacts There are charged ions in motion all over our body and they generate magnetic field, which interferes with the MR imaging.

Off-Resonance Effect or Chemical Shift Effect H nuclei in fat (lipid) feel slightly different magnetic field than those in water under the same magnetic field strength B 0. This is a significant artifact at the boundary between fat and water, but no much in the brain or the grey matter. It is more in EPI than conventional MR imaging.

Exercise Familiarize with the freely available MATLAB based software package Statistical Parametric Mapping (SPM): Familiarize with the freely available software package FSL (on Linux or Windows) at

References R. B. Buxton, Introduction to Functional Magnetic Resonance Imaging, 2e, Cambridge University Press, Cambridge, UK, R. A. Poldrack, J. A. Mumford and T. E. Nichols, Handbook of Functional MRI Data Analysis, Cambridge University Press, Cambridge, New York, 2011.

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