Peter A. Bandettini, Ph.D. Section on Functional Imaging Methods Laboratory of Brain and Cognition http://fim.nimh.nih.gov & Functional MRI Facility http://fmrif.nimh.nih.gov [email protected]“Optimizations” (or at least improvements) in fMRI Methodology Interpretation Applications Technology Coil arrays High field strength High resolution Novel functional contrast Functional Connectivity Multi-modal integration Pattern-effect imaging Real time feedback Task design Fluctuations Dynamics Spatial patterns Healthy Brain Organization Clinical Pathology In general fMRI before any optimizations (fall of 1991)
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fMRI before any optimizations (fall of 1991)...How brief of a stimulus can one give?! 5! 10! 15! 20! Time (sec)! 1000 msec! 100 msec! 34 msec! R. L. Savoy, et al., Pushing the temporal
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Peter A. Bandettini, Ph.D.!!
Section on Functional Imaging Methods!
Laboratory of Brain and Cognition!http://fim.nimh.nih.gov!
J. L. Boxerman, P. A. Bandettini, K. K. Kwong, J. R. Baker, T. L. Davis, B. R. Rosen, R. M. Weisskoff, The intravascular contribution to fMRI signal change: monte carlo modeling and diffusion - weighted studies in vivo. Magn. Reson. Med. 34, 4-10 (1995).
b = 0!
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b = 10!
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Arterial inflow!(BOLD TR < 500 ms)!
Hemodynamic Specificity!
High Field Tradeoffs
• Increased SNR
• Increased functional contrast
• Ability to reduce voxel volume
• Reduced intravascular signal
• At standard resolution, enhanced
sensitivity to fluctuations
• Increased SAR
• Decreased B0 and B1 homogeneity
• (still somewhat prohibitive)
• Increased costs and effort
• At standard resolution, enhanced
sensitivity to fluctuations
Coil Arrays
16 channel parallel receiver coil!
GE birdcage! GE 8 channel coil! Nova 8 channel coil!
8 channel parallel receiver coil!
J. Bodurka, et al, Magnetic Resonance in Medicine 51 (2004) 165-171.!
Sensitivity vs. Time needed to scan
K. Murphy, J. Bodurka, P. A. Bandettini, How long to scan? The relationship between fMRI temporal signal to noise and the necessary scan duration. NeuroImage, 34, 565-574 (2007) J. Bodurka, F. Ye, N Petridou, K. Murphy, P. A. Bandettini, NeuroImage, 34, 542-549 (2007)
Temporal Signal to Noise Ratio (TSNR) vs. Signal to Noise Ratio (SNR)
3T, birdcage: 2.5 mm3
3T, 16 channel: 1.8 mm3 7T, 16 channel: 1.4 mm3
suggested voxel volume
Going to High Spatial Resolution
MRI vs. fMRI!MRI! fMRI!
one image!
many images !(e.g., every 2 sec for 5 mins)!
high resolution!(1 mm)!
…!
T2* decay!
EPI Readout Window!� 20 to 40 ms!
Single Shot Echo Planar Imaging (EPI)! Multishot Imaging
T2* decay!
EPI Window 1!
T2* decay!
EPI Window 2!
Excitations 1 2 4 8 Matrix Size 64 x 64 128 x 128 256 x 128 256 x 256
Multi Shot EPI!
30 ms! 10 sec !to !1 min!
Partial k-space imaging
T2* decay!
EPI Window!
A. Jesmanowicz, P. A. Bandettini, J. S. Hyde, Single shot half k-space high resolution EPI for fMRI at 3T. Magn. Reson. Med. 40, 754-762 (1998).
A. Jesmanowicz, P. A. Bandettini, J. S. Hyde, Single shot half k-space high resolution EPI for fMRI at 3T. Magn. Reson. Med. 40, 754-762 (1998). ≈ 5 to 30 ms
Pruessmann, et al. (and Sodickson et al)
SENSE Imaging
3T single-shot SENSE EPI using 16 channels: 1.25x1.25x2mm Cheng, et al. (2001) Neuron,32:359-374
Technology
Scalebar = 0.5 mm
Orientation Columns in Human V1 as Revealed by fMRI at 7T
Phase 0° 180°
Phase Map
Yacoub et al. PNAS 2008
Going to High Temporal Resolution
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P. A. Bandettini, K. K. Kwong, T. L. Davis, R. B. H. Tootell, E. C. Wong, P. T. Fox, J. W. Belliveau, R. M. Weisskoff, B. R. Rosen, (1997). “Characterization of cerebral blood oxygenation and flow changes during prolonged brain activation.” Human Brain Mapping 5, 93-109.!
How rapidly can one switch on and off?
P. A. Bandettini,, Functional MRI using the BOLD approach: dynamic characteristics and data analysis methods, in "Diffusion and Perfusion: Magnetic Resonance Imaging" (D. L. Bihan, Ed.), p.351-362, Raven Press, New York, 1995.
Blamire et al.!
Blamire, A. M., et al. (1992). �Dynamic mapping of the human visual cortex by high-speed magnetic resonance imaging.� Proc. Natl. Acad. Sci. USA 89: 11069-11073.
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Bandettini, et al., The functional dynamics of blood oxygenation level contrast in the motor cortex, 12'th Proc. Soc. Magn. Reson. Med., New York, p. 1382. (1993).
How brief of a stimulus can one give?!
5! 10! 15! 20!Time (sec)!
1000 msec!100 msec!34 msec!
R. L. Savoy, et al., Pushing the temporal resolution of fMRI: studies of very brief visual stimuli, onset variability and asynchrony, and stimulus-correlated changes in noise, 3'rd Proc. Soc. Magn. Reson., Nice, p. 450. (1995). !
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11026–11031 PNAS September 26, 2000 vol. 97 no. 20 P. A. Bandettini, (1999) "Functional MRI" 205-220.!
Choosing a Flip Angle Physiological noise effects on the flip angle selection in BOLD fMRI
J. Gonzalez-Castillo a,⁎, V. Roopchansingh b, P.A. Bandettini a,b, J. Bodurka c
a Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USAb Functional MRI Facility, National Institute of Mental Health, National Institutes of Health, 10 Center Dr, Bethesda, MD 20892, USAc Laureate Institute for Brain Research, 6655 South Yale Avenue, Tulsa, OK 74136, USA
a b s t r a c ta r t i c l e i n f o
Article history:Received 18 August 2010Revised 29 October 2010Accepted 4 November 2010Available online 10 November 2010
This work addresses the choice of imaging flip angle in blood oxygenation level dependent (BOLD) functionalmagnetic resonance imaging (fMRI). When noise of physiological origin becomes the dominant noise sourcein fMRI timeseries, it causes a nonlinear dependence of the temporal signal-to-noise ratio (TSNR) versussignal-to-noise ratio (SNR) that can be exploited to perform BOLD fMRI at angles well below the Ernst anglewithout any detrimental effect on our ability to detect sites of neuronal activation. We show, bothexperimentally and theoretically, that for situations where available SNR is high and physiological noisedominates over system/thermal noise, although TSNR still reaches it maximum for the Ernst angle, reductionof imaging flip angle well below this angle results in negligible loss in TSNR. Moreover, we provide a way tocompute a suggested imaging flip angle, which constitutes a conservative estimate of the minimum flip anglethat can be used under given experimental SNR and physiological noise levels. For our experimentalconditions, this suggested angle equals 7.63° for the grey matter compartment, while the Ernst angle=77°.Finally, using data from eight subjects with a combined visual-motor task we show that imaging at angles aslow as 9° introduces no significant differences in observed hemodynamic response time-course, contrast-to-noise ratio, voxel-wise effect size or statistical maps of activation as compared to imaging at 75° (an angleclose to the Ernst angle). These results suggest that using low flip angles in BOLD fMRI experimentation toobtain benefits such as (1) reduction of RF power, (2) limitation of apparent T1-related inflow effects,(3) reduction of through-plane motion artifacts, (4) lower levels of physiological noise, and (5) improvedtissue contrast is feasible when physiological noise dominates and SNR is high.
A common practice in gradient recalled-echo (GRE) functionalmagnetic resonance imaging (fMRI) is to select the imaging flipangle to be equal to the Ernst angle (Ernst and Anderson, 1996) forgrey matter. The premise is to select the Ernst angle to maximizethe grey matter signal-to-noise ratio (SNR). Although thisapproach has proven beneficial for spoiled gradient echo anatomicallyoriented applications of MRI, in which physiological noise does notdominate or even contribute significantly (i.e. SNRb50 or in non livingsamples), the same might not be necessarily true for fMRI, in whichnon-thermal noise dominates (Kruger and Glover, 2001; Triantafyllouet al., 2005).
FMRI detects neuronal activity-induced subtle temporal MRIsignal fluctuations that have their origin in the BOLD (BloodOxygenation Level Dependent) phenomenon (Ogawa et al., 1993).These time series contain noise. Specifically, physiological noise ispresent and represents a confounding factor in BOLD fMRI data
(Kruger and Glover, 2001). Depending on the imaging voxel volumeand available SNR, physiological noise frequently becomes thedominant noise source present in fMRI time courses (Bodurkaet al., 2007). The quality of functional MRI data can be characterizedin terms of temporal-SNR (TSNR). This metric is defined andcomputed on a voxel-wise basis as the ratio of the mean steady-state signal of the fMRI time-series to the voxel temporal standarddeviation (Parrish et al., 2000). While SNR is independent ofphysiological noise contributions (i.e., in EPI, an image is collectedwithin 40 ms–faster than most physiologic process–thus minimizingeffects of temporal variations of these), TSNR shows a non-lineardependence on physiological noise contribution. Based on this non-linear dependence of TSNR with physiological noise and the fact thatphysiological noise is MR-signal strength dependent (Kruger andGlover, 2001; Triantafyllou et al., 2005), we hypothesize that thebehavior of SNR and TSNR as a function of imaging flip angle mightdiffer; and that such differences might be exploited to perform fMRIexperiments at imaging angles well below the Ernst angle.
This work studies, both theoretically and experimentally, the TSNRdependence on the flip angle. We provide evidence that, in thepresence of physiologic noise, the TSNR does not follow therelationship defined by the Ernst equation. In fact, we show that
How do we typically select flip angle? Ernst Angle…
Θ = Cos-1 (e -TR/T1)
Fig. 2. (A) TSNR vs. Flip angle for T1=T1,GM=1.34 s, SNRo=SNRo,GM=652 and different values of ! ranging from 0 to 0.05. For each curve, a square marks the angle below the Ernstangle for which TSNR has decreased to 50% from its maximum value ("50%). (B) Evolution of "50% with !. The higher the amount of physiological noise present, the flatter the TSNRcurve and consequently the lower the angle for which TSNR reaches 50% of its maximum value.
Fig. 3. Simulations of the suggested fMRI flip angle ("S). The black dotted line shows a linear behavior for the Silicone Oil Phantom. The red and blue continuous lines show behaviorfor grey and white matter respectively. Ernst angle for these two tissue compartments is marked with filled dots, while other exemplary angles are masked as transparent dots. Thesuggested flip angle for both tissue compartments are also marked in each curve as filled squares with black outline.
2767J. Gonzalez-Castillo et al. / NeuroImage 54 (2011) 2764–2778
better contrast at lower flip angles translates in easier segregation oftissue compartments.
Discussion
Physiological noise is a major source of undesired variance inBOLD fMRI time courses in a vast majority of experimental situations(Kruger and Glover, 2001; Kruger et al., 2001; Triantafyllou et al.,2005; Bodurka et al., 2007). We have investigated, both theoreticallyand experimentally, the effect that MR-signal strength-dependentphysiological noise exerts on BOLD fMRI temporal signal to noise
ratio (TSNR) as a function of the flip angle in situations wherephysiological noise constitutes a dominant source of time coursevariance. We have scanned 8 subjects at a commonly used BOLDfMRI voxel volume of 3.75!3.75!4 mm3, where physiological noiseis the dominant source of time course variance (Bodurka et al.,2007); and physiological noise introduces a non-linear dependencein TSNR, which translates into a flattening of the TSNR vs. flip anglecurve. We have also demonstrated that this TSNR behavior can beexploited to perform BOLD-fMRI at flip angles other than the Ernstangle with no detrimental effects in our ability to detect statisticallysignificant neuronal activations.
Fig. 7. Averaged hemodynamic response across all eight subjects for all flip angles in three different anatomically defined ROIs: right visual cortex, left visual cortex and left primarymotor cortex. The top panel shows 3D renderings of the ROIs. Themiddle panel shows estimations of the hemodynamic response without intensity normalization (i.e., only constant,linear and quadratic trends were removed). The bottom panel shows estimations of hemodynamic response in terms of signal percent change. These were obtained by means ofintensity normalization prior to the detrending step.
2772 J. Gonzalez-Castillo et al. / NeuroImage 54 (2011) 2764–2778
and/or elapsed time between scans; they provide support for theclaim that using angles other than the Ernst angle do not cause anydisadvantage when attempting to detect BOLD related activations, atleast for the task and the range of angles under consideration in thisstudy.
Evaluation of plausible flip angle effects on the estimation ofregression coefficients (!) at single-subject statistical analysis alsorendered not significant. This result suggests that second levelstatistical analysis (group analysis), which uses as input ! coefficientsfrom individual subjects, should not be negatively affected by the useof angles other than the Ernst angle. Scatter plot and correlationanalysis results show that a voxel-wise linear relation exists between! coefficients at "=75°(closest available angle to the Ernst angle forGM at 3 T and TR=2 s) and all other angles. Moreover, we showedthat the slope (S) and constant term (C) of this linear relationship arenot significantly different from the ideal case (S=1, C=0) in whichvoxel-wise ! coefficients would be identical across flip angles.Although deviations from the ideal case exists, the fact that theseare not significant or consistent across ROIs, suggest that thesevariations are solely the result of random inter-scan variations notaccounted for by the regression analysis; and not a systematic effectattributable to changes in the flip angle.
Although the analysis on how imaging flip angle affects hemody-namic response, CNR, activation extent and ! coefficients wasperformed on data collected using a specific experimental sensorimotorepoch design, we believe that the main conclusion of such analysis–namely that flip angle has no systematic effect on the ability to detectBOLD-based neuronal activity–remains valid for other types of fMRIexperimental paradigms such as event-related designs, high-ordercognitive tasks, etc. We construct this claim on the base that changes to
the experimental task are not expected tomodify the TSNR vs.flip anglenon-linear relationship described in this work. Nonetheless, prior toadoption of a low imaging angle for a set of experiments, researchersare encouraged to confirm that physiological noise is the dominantsource of noise in their setting (#p/#oNN1) and that SNR levels aresufficiently high. One way to obtain such confirmation is to computethe suggested imaging flip angle using Eq. (10) (or its non-approximated version Eq. (9)). Inputs to these formulas includeexperimental measures of physiological noise and SNR levels specificto the experimental settings under consideration. If both requirementsare satisfied, the suggested flip angle will be lower than the Ernst angle.On the other hand, if one or both of these requirements are not satisfiedthe computed suggested angle will be equal or greater than the Ernstangle (see Fig. 4 for a case when physiological noise decreases to levelsin which it is no longer the dominant noise source) and researchersshould consider using the Ernst angle. As a general guideline,experiments conducted at field strengths equal or greater than 3Tesla, using receiver array-coils of eight or more elements and voxelssize in the vicinity of 50 mm3 (3.75!3.75!4.00 mm) will lead tosuggested imaging flip angles well below the Ernst angle.
We believe these results have important implications for exper-imental fMRI, as the use of small flip angles provides importantadditional benefits such as better tissue contrast, less inflow effects(Gao et al., 1996), less through-plane motion artifacts, lowerphysiological noise levels, shorter scanning times, and reduced levelsof radio-frequency (RF) energy deposition. All these benefits arisethrough the following mechanisms. The flip angle for an MRexperiment is computed by:
θ = γ ! RF pulse amplitude ! RF pulse duration
Fig. 12. (A) Experimental and Theoretical curves describing dependence of tissue contrast with flip angle for three tissue contrast of interest: GM vs. WM (ΔSGM,WM), GM vs. CSF(ΔSGM,CSF), and WM vs. CSF (ΔSWM,CSF). (B) Axial slices, after steady-state has been reached, for all acquired flip angles for an exemplary subject.
2776 J. Gonzalez-Castillo et al. / NeuroImage 54 (2011) 2764–2778
Effect of Slice Thickness on TSNR
P. S. F. Bellgowan, P. A. Bandettini, P. van Gelderen, A. Martin, J. Bodurka, Improved BOLD detection in the medial temporal region using parallel imaging and voxel volume reduction. NeuroImage, 29, 1244-1251 (2006)
Methodology
Interpretation Applications
Technology High field strength Coil arrays High resolution Novel functional contrast
P. A. Bandettini, A. Jesmanowicz, E. C. Wong, J. S. Hyde, Processing strategies for time-course data sets in functional MRI of the human brain. Magn. Reson. Med. 30, 161-173 (1993).
Neuronal Activation Input Strategies
1. Block Design
2. Frequency Encoding
3. Phase Encoding
4. Event-Related
5. Orthogonal Block Design
6. Free Behavior Design.
Tapping left and right fingers at two different “on/off” frequencies
P. A. Bandettini, A. Jesmanowicz, E. C. Wong, J. S. Hyde, Processing strategies for time-course data sets in functional MRI of the human brain. Magn. Reson. Med. 30, 161-173 (1993).
Neuronal Activation Input Strategies
1. Block Design
2. Frequency Encoding
3. Phase Encoding
4. Event-Related
5. Orthogonal Block Design
6. Free Behavior Design.
E. A. DeYoe, P. A. Bandettini, J. Nietz, D. Miller, P. Winas, Functional magnetic resonance imaging (FMRI) of the human brain. J. Neuroscience Methods 54, 171-187 (1994).
E. A. DeYoe, G. Carman, P. Bandettini, G. S., W. J., R. Cox, D. Miller, J. Neitz, Mapping striate and extrastriate visual areas in human cerebral cortex. Proc. Nat'l. Acad. Sci. 93, 2282-2386 (1996).
E. A. DeYoe, G. Carman, P. Bandettini, G. S., W. J., R. Cox, D. Miller, J. Neitz, Mapping striate and extrastriate visual areas in human cerebral cortex. Proc. Nat'l. Acad. Sci. 93, 2282-2386 (1996).
Neuronal Activation Input Strategies
1. Block Design
2. Frequency Encoding
3. Phase Encoding
4. Event-Related
5. Orthogonal Block Design
6. Free Behavior Design.
R. L. Buckner, P. A. Bandettini, K. M. O'Craven, R. L. Savoy, S. E. Peterson, M. E. Raichle, T. L. Brady, B. R. Rosen, fMRI detection and time course of distributed cortical activations during single trials of a cognitive task. Proc. Nat'l. Acad. Sci. USA 93, 14878-14883 (1996).
P. A. Bandettini, R. W. Cox. Functional contrast in constant interstimulus interval event - related fMRI: theory and experiment. Magn. Reson. Med. 43: 540-548 (2000). !
20, 20! 12, 2! 10, 2! 8, 2! 6, 2! 4, 2! 2, 2!
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P. A. Bandettini, R. W. Cox. Functional contrast in constant interstimulus interval event - related fMRI: theory and experiment. Magn. Reson. Med. 43: 540-548 (2000). !
R. M. Birn, R. W. Cox, P. A. Bandettini, Detection versus estimation in Event-Related fMRI: choosing the optimal stimulus timing. NeuroImage 15: 262-264, (2002).
Estimation accuracy vs. average ISI
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R. M. Birn, R. W. Cox, P. A. Bandettini, Detection versus estimation in Event-Related fMRI: choosing the optimal stimulus timing. NeuroImage 15: 262-264, (2002).
fMRI during tasks that involve brief motion!
motion! BOLD response!
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R. M. Birn, P. A. Bandettini, R. W. Cox, R. Shaker, Event - related fMRI of tasks involving brief motion. Human Brain Mapping 7: 106-114 (1999). !
Speaking - Blocked Trial!
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R. M. Birn, P. A. Bandettini, R. W. Cox, R. Shaker, Event - related fMRI of tasks involving brief motion. Human Brain Mapping 7: 106-114 (1999). !
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Overt Responses - Simulations!
R.M. Birn, R. W. Cox, P. A. Bandettini, NeuroImage, 23, 1046-1058 (2004) !
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Blocked design (30s/30s)!
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Neuronal Activation Input Strategies
1. Block Design
2. Frequency Encoding
3. Phase Encoding
4. Event-Related
5. Orthogonal Block Design
6. Free Behavior Design.
Example of a Set of Orthogonal Contrasts for Multiple Regression!
J. Gonzalez-Castillo, Z. Saad, D. A. Handwerker, P. A. Bandettini, Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis. Proceedings of the National Academy of Sciences 109, 14: pp. 5487-5492 (2012)
in Resting State fMRI.!Res0ng#state#clustering#in#mul0ple#and#single#subjects.#
• Mul=9echo"denoising"• Hierarchical"clustering##
P. Kundu, S. J. Inati, J. W. Evans, W.-M. Luh, P. A. Bandettini, Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI. NeuroImage 60, pp. 1759-1770 (2012)
Rest: seed voxel in motor cortex
Activation: correlation with reference function
B. Biswal et al., MRM, 34:537 (1995)
Resting State Correlations
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("resting state" OR fluctuations OR "spontaneous oscillations" OR "endogenous oscillations") AND fMRI
Endogenous Oscillations
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De Luca, Neuroimage 29(4) 2006
Visual
Visuospatial Executive
Sensory Auditory
Dorsal Pathway
Ventral Pathway
Sources of time series fluctuations • Blood, brain and CSF pulsation
• Vasomotion
• Breathing cycle (B0 shifts with lung expansion)
• Bulk motion
• Scanner instabilities
• Changes in blood CO2 (changes in breathing)
• Spontaneous neuronal activity
Noise and Fluctuations
Fig. 4. Pie charts showing the fMRI data variance explained (VE, %, upper bold) by nonthermal noise sources 1–4, thermal noise and spontaneous activity. We also show fMRI signal change (SC, %, lower italic) attributed to the same noise sources. Average (S.E.) values across subjects are shown. The contribution of thermal noise at the ROI level was negligible.
Bianciardi et al. Magnetic Resonance Imaging 27: 1019-1029, 2009
Toes Fingers Thumb Eyebrow Tongue
Sources of time series fluctuations: • Blood, brain and CSF pulsation
• Vasomotion
• Breathing cycle (B0 shifts with lung expansion)
• Bulk motion
• Scanner instabilities
• Changes in blood CO2 (changes in breathing)
• Spontaneous neuronal activity
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R.M. Birn, J. A. Diamond, M. A. Smith, P. A. Bandettini, NeuroImage, 31, 1536-1548
Spontaneous changes in respiration and end-tidal CO2
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