basic physiology of fmri: signal and noise materials...(cardiac, respiration) subject motion scanner...
TRANSCRIPT
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Basic physiology of fMRI: signal and noise
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Overview
• Brief overview of fMRI • Contrast mechanisms
– Source of the fMRI signal
• Sources of Noise (& corrections) – Motion
– Cardiac
– Respiration
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Brain activity during cued finger tapping
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Measuring Brain Function with MRI
Task
Neuronal Activity
Red Blood Cells
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How can we see brain function with MRI?
red blood cells
oxygenated
deoxygenated
L. Pauling, C. D. Coryell, Proc.Natl. Acad. Sci. USA 22, 210-216, 1936.
Oxygenated and deoxygenated red blood cells have different magnetic properties
diamagnetic
paramagnetic
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Detecting “activation”
Capillaries!
Veins!Arteries!
Capillaries!
Veins!Arteries!
χ1 χ2 χ2 χ2
ΔS =
0
0.2
0.4
0.6
0.8
1
1.2
0 50 100 150 200
M0a e-t/T2*a - M0r e-t/T2*r
time
Sig
nal
ΔS S0
= M0a
M0r e-tΔR2* - 1
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Measuring Brain Function with MRI
Task
t
t
task Hemodynamics Neuronal Activity
Red Blood Cells
Task Blood Flow deoxy-Hb MRI signal
BOLD = Blood Oxygenation Level Dependent
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The Blood Oxygenation Level Dependent Response
Task
neuronal activity
BF
deoxy-Hb
MR signal
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The Blood Oxygenation Level Dependent Response
Task
neuronal activity
BF
HbO2 deoxy-Hb
MR signal
CMRO2 BV - - +
0 20 40 60
Time (sec)
Sig
nal
0 5 10 15 Time (sec)
Sig
nal
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Temporal dynamics of fMRI signal change
Delay
Activation amplitude
Arbitrary Scale
+ 2 sec
- 2 sec
0 sec 0 10 20 30 40 50
-2 -1.5 -1 -0.5 0 0.5 1 1.5 2
Num
ber o
f Vox
els
Delay (sec)
t
task fMRI signal
0 10 s
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Functional Magnetic Resonance Imaging (fMRI)
Typical MRI t
Functional MRI
Look for changes in MRI signal over time
Task Blood Flow MRI signal deoxy-Hb
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Brain activity during cued finger tapping
t
t
task
Map the changes in MRI signal over time
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Functional MRI
t
t
Task-related Neuronal Activity
Physiologic noise (cardiac, respiration)
Subject motion
Scanner instabilities Image reconstruction errors
Spontaneous Neuronal Activity
Hemodynamics resting state
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Problem: Subject Motion
motion
t
t
t
Signal changes occur at edges
t
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Correcting for subject motion
• Image registration
t = 0 t = 1
• Prevent Motion
• Regress out motion-related changes
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Problem: motion during the volume
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Problem: motion during the volume
slices are actually acquired like this… expected acquisition:
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Problem: motion during the volume
Potential solution: Prospective motion correction
slice tracks with the motion
• C.C. Lee, et al., Magn. Res. Med., 39, 1998. • H.A. Ward, et al., Magn. Res. Med., 43, 2000. • O. Speck, et al., Magma 19, 2006.
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Physiological noise
0 40 80 120 160 200 240 280 320 time (s)
Cardiac
M.S. Dagli et al., NeuroImage 9, 1999
Respiration
time 00 TIME = 110 s
ΔΦ =90 o 400
200
B0
Field Map
Figure courtesy of J. Bodurka
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Can filtering (<0.1Hz) reduce cardiac noise?
0 5 10 15 20 time (s)
Sign
al
Cardiac fluctuation (1.1 Hz) Sampled every TR (2s)
0 0.5 1 1.5 2 Frequency (Hz)
0
0.1
0.2
0.3
Pow
er
• Not always: Aliasing
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Correction of physiological noise
RETROICOR (G. Glover et al., Magn. Reson. Med. 44, 2000.)
Pulse Oximeter
0 1 2 3 4 5 6 7 8 9 10 time (s)
Respiration
MR Images
φc
φr
sin( φc )
cos( φc )
sin( 2φc )
cos( 2φc )
sin( φr )
cos( φr )
sin( 2φr )
cos( 2φr )
Additional Regressors:
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Correction of physiological noise
time
Sig
nal
Reshuffle the data based on its cardiac or respiration phase
0 1 2 3 4 5 6
Sig
nal
phase
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Correction: Cardiac + Respiration
X. Hu et al., Magn. Res. Med. 1995
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At what stage should physio correction be done?
• Preprocessing – Motion correction – Physiological noise correction – Slice time correction – Nuisance Regression – Spatial Smoothing – Convert to percent signal change – Temporal filter
• Define ROI (seed) • Average EPI time course over ROI • Regression T.B. Jones et al., Neuroimage 42, 2008
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Physio. fluctations can occur at low frequencies
Variations in breathing during rest ΔBOLD signal
PETCO2
BOLD (GM)
BOLD (WM)
R.G. Wise et al., NeuroImage 21, 2004
ΔPETCO2 correlated w/ ΔBOLD
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Resting fluctuations in respiration
RVT = Respiration Volume per Time
50 100 150 200 250 300 350
0
6
|Z|
group (n=11)
RVT-related changes
RVT
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Heart Rate
Birn et al. (unpublished)
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RVHRcor (Respiration Volume + Heart Rate)
C. Chang et al., Neuroimage 2009
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Nuisance Regression
H.J. Jo et al., NeuroImage 52, 2010
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The effect of global signal regression
The global signal is highly correlated w/ RVT
-1
-0.5
0
0.5
1
CC
: RV
T ~
glob
al s
igna
l
without global regression
with global regression
Connectivity maps
0.5
0.3
-0.1
0
(separate study, n = 18)
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Global Signal Regression
K. Murphy, et al., Neuroimage, 2008
Can introduce anti-correlations
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Global Signal Regression
Z.S. Saad, et al., Brain Connectivity, 2012
Can alter group differences …under certain conditions
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Nuisance Regression
H.J. Jo et al., NeuroImage 52, 2010
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PSTCor (Phase-shifted Soft Tissue Corr.)
J.S. Anderson et al., HBM 32, 2011
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“FIX” (FMRIB’s ICA-based X-noisifier)
L. Griffanti, et al., Neuroimage 2014
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ICA-AROMA
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ICA-AROMA
R.H.R. Pruim et al., NeuroImage 112 (2015)
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Tools to correct for physiological noise
• Filtering - Works only if TR is short enough (< 400ms)
• IMPACT (Chuang et al., 2001) – if TR short enough
• Retrospective correction (k-space) (X. Hu et al., 1995)
• RETROICOR (Glover et al., 2000)
• CORSICA (V. Pelbarg, et al., 2007)
• PESTICA (E.B. Beall, et al., 2007)
• RVTcor (R.M. Birn, et al., 2006) • RVHRcor (C. Chang, et al., 2009) • ANATICOR (H-J. Jo, et al., ) • APPLECOR, PEARCOR (M Marx, et al., 2013) • PSTCor (J.S. Anderson, et al., 2011) • CompCor (Y. Behzadi, et al., 2007)
• FIX (L. Griffanti, et al., 2014)
• ICA-AROMA (###, et al., 2015)
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Should we perform physio corrections?
• Reduces fluctuations related to heart beat and respiration – Reduce false positives – Reduce false negatives
• Some physiological fluctuations are
associated with neuronal activity – E.g. Heart rate variability
This is still an open question in the field
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Signal / Physiologic Noise
Tem
pora
l Sig
nal t
o N
oise
Rat
io
TSNR vs SNR
Signal-to-Noise Ratio
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J. Bodurka
TSNR vs SNR