functional brain signal processing: eeg & fmri lesson 12 kaushik majumdar indian statistical...
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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 B0 is high transverse magnetic field M0 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.
0SNR M VT
Point Spread Function and Gibb’s Phenomenon
Buxton, 2009
T2* Time Effect
Since , if acquisition time is increased the SNR will be improved. But we also have .
So acquisition time is bounded above by T2*
relaxation time.
0SNR M VT
*2 2 1T T T
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 T1 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 B0. 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): http://www.fil.ion.ucl.ac.uk/spm/
Familiarize with the freely available software package FSL (on Linux or Windows) at http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
References
R. B. Buxton, Introduction to Functional Magnetic Resonance Imaging, 2e, Cambridge University Press, Cambridge, UK, 2009.
R. A. Poldrack, J. A. Mumford and T. E. Nichols, Handbook of Functional MRI Data Analysis, Cambridge University Press, Cambridge, New York, 2011.
THANK YOU
This lecture is available at http://www.isibang.ac.in/~kaushik