# Presentation: 247173

## Section on Functional Imaging Methods

**(May 2003- November 2007)**
**Peter A. Bandettini, Ph.D.**

## ?

**Hemodynamics**

**?**

**?**

**?**

**Measured Signal**

**Noise**

**?**

## Slide 3

## Slide 4

## Dynamics

**Motivation:**
**To understand neuronal and non-neuronal influences on the fMRI signal.**
**Studies:**** **
**Modulate “on” duration, “off” duration, and duty cycle of visual cortex activation.**
**Neuronal and Hemodynamic Modeling**

## Brief “on” periods produce larger increases than expected.

- measured

- linear

- Signal

- Brief “on” periods produce **larger** increases than expected.

- Linearity

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- Stimulus Duration (s)

*linear*

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**R. M. Birn, Z. Saad, P. A. Bandettini, NeuroImage, 14: 817-826, (2001)**

- time (s)

## Varying the Duty Cycle

*Deconvolved  Response*

- R.M. Birn, P. A. Bandettini, *NeuroImage*, **27, 70-82 (2005) **

## Simulation of Hemodynamic Mechanisms (Balloon model)

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- Duty Cycle

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- Duty Cycle

**Linearity**

**BOLD Signal**

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**a**

**f**

**g**

**h**

**b**

**c**

**d**

**e**

**E(f)=Lin, ********V=0**

**E(f)=Lin, ********V**

**E(f)=NL, ********V=0**

**E(f)=NL , ********V**

**E(f) = oxygen extraction fraction**
**V = blood volume**

## Simulation of Neuronal Mechanisms

**Adaptation**

**Adaptation **
**+ refractory**

**Adaptation **
**+ refractory **
**+ OFF response**

**Linear**

- 1

- 1

- 1

- 2

- 1

**BOLD Signal**

## Dynamics

**Conclusion:**** **
**Nonlinearities are not fully explained by the Balloon model.**
**“****OFF” modulation sub-linearity suggests that blood volume change is not slower than flow change. **
**Future:**** **
**Modulate neural activity or hemodynamic variables independently.**
**Measure flow, volume to help constrain balloon model.**
**Determine spatial and across-subject heterogeneity.**

## 2. Fluctuations

**Motivation:**** **
**Applications of connectivity mapping (autism, schizophrenia, Alzheimer’s, ADHD).**
**Distinguish neuronal activity-related fluctuations from non-neuronal physiological fluctuations.**
***-reduce false positives in resting state connectivity maps ***
***-increase functional contrast to noise for activation maps***
**fMRI *****activation magnitude *****calibration using fluctuations rather than hypercapnic or breath-hold stress.**
**Studies:**
**Time course of respiration volume per unit time (RVT)**
**The Respiration Response Function (RRF)**
**FMRI Calibration using RRF**

## Sources of time series fluctuations: 

**Blood, brain and CSF pulsation**
**Vasomotion**
**Breathing cycle (B****0**** shifts with lung expansion)**
**Bulk motion**
**Scanner instabilities**
**Changes in blood CO****2 ****(changes in breathing)**
**Spontaneous neuronal activity**

## Estimating respiration volume changes

- Respiration

- Respiration Volume / Time (**RVT**)

- time (s)

**RVT precedes end tidal CO****2**** by 5 sec.**

## Respiration induced signal changes

***Rest***

***Breath-holding***

- (N=7)

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- 9

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- 4.5

- 2

- Rest (%)

- Breath hold (%)

- CC = 0.76

## RVT Correlation Maps &Functional Connectivity Maps

- Resting state correlation with
- signal from posterior cingulate

*Group (n=10)*

- -10

- 10

- Z

- Resting state correlation with
- RVT signal

## Effect of Respiration Rate Consistency on Resting Correlation Maps

- 10

- Z

- -10

- 10

- Z

- Constant Respiration Rate

*Group (n=10)*

- Spontaneously Varying Respiration Rate

- Blue: deactivated
- network

**Lexical Decision **
**Making Task**

## Respiration Changes vs. BOLD

- RVT

- fMRI Signal

*How are the BOLD changes related to respiration variations?*

- ?

## fMRI response to a single Deep Breath

*Respiration*

- 40s

**...**

- Respiration
- Response
- Function
- (**RRF**)

***deconv.***

- R.M. Birn, M. A. Smith, T. B. Jones, P. A. Bandettini, *NeuroImage*, **(in press) **

## Breath-holding

- time (s)

- Signal (%)

- 20s

- 40-60s

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- 300

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- Rate Changes

- 20s

- 40s

- time (s)

- Signal (%)

- Depth Changes

- 20s

- 40s

- time (s)

- Signal (%)

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## BOLD magnitude calibration

- Before
- Calibration

- After
- Calibration

*Respiration-induced ****S*

- Breath
- Hold

- Rest

- Depth
- Change

- Rate
- Change

## 2. Fluctuations

**Conclusion:**** **
**RVT maps resemble connectivity maps.**
**Constant breathing is effective in reducing fluctuations.**
**Respiration Response Function is characterized.**
**Breath hold, rate changes, depth changes, AND resting fluctuations can be used to calibrate BOLD magnitude. **
**Future:**
**Test calibration effectiveness.**
**Compare ICA derived maps before and after RVT regression or breathing rate controls.**

## 3. Experimental Design

**Motivation:**** **
**Guides for *****individual***** subject scanning at the limits of detectability, resolution, available time, and subject performance.**
**Studies:**
**Overt response timing**
**Suggested resolution**

## Overt Responses - Simulations

- R.M. Birn, R. W. Cox, P. A. Bandettini, *NeuroImage,* 23, 1046-1058 (2004)

**SD = stimulus duration**

**More Motion Artifacts**

**Better BOLD Detection**

## Overt Responses

## Finding the “suggested voxel volume”

**Temporal Signal to Noise Ratio (TSNR) vs. Signal to Noise Ratio (SNR)**

**3T, birdcage: ****	****2.5 mm****3**
**3T, 16 channel:****	****1.8 mm****3**
**7T, 16 channel:****	****1.4 mm****3**

## 3. Experimental Design

**Conclusion:**** **
**Overt response paradigms are experimentally verified (blocked, 10 on/ 10 off is best). **
**The “suggested voxel volume” concept shows the importance of TSNR in gray matter rather than SNR.**
**Future:**
**Implement rapid “suggested voxel volume” calculation at scanner, based on TSNR measure.**

## 4. Pattern-Information Analysis

**Motivation: **
**Classical fMRI analysis: **
***	******Is a region activated during a task?***
**Pattern-information analysis: **
***	******Does a region carry a particular kind of ******	******information?***
**Study:**
**Pattern-Information Mapping**
**Dis-similarity matrix**

## Pattern Information 

**Mapping**

**From fixed ROI**

## ...

**response**
**patterns**

**stimuli**

**...**

**...**

**ROI in Brain**

**compute dissimilarity**
- (1-correlation across space)

**Dissimilarity Matrix**
**Creation**

- N. Kriegeskorte, et al (in review)

## Visual Stimuli

## Human IT(1000 visually most responsive voxels)

**Human IT****(1000 visually most responsive voxels)**

## N. Kriegeskorte, et al (in review)

## 4. Pattern-Information Analysis

**Conclusion: **
**Useful for mapping and comparing voxel wise patterns that may be missed with classical approaches.**
**Future:**
**Spatial scale/distribution of most informative patterns with learning, categorization?**
**Careful comparisons to mapping approaches.**
**High resolution, high field.**

## 5. Neuronal Current MRI

**Motivation:**** **
**Direct fMRI of neuronal activity.**
**Studies:**
**7T and 3T**

## Neuronal Cell Cultures at 7T

- N. Petridou, D. Plenz, A. C. Silva, J. Bodurka, M. Loew, P. A. Bandettini, *Proc. Nat'l. **Acad. Sci. USA*. 103, **16015-16020 (2006).**

**-TTX**
**-no TTX**

## 5. Neuronal Current MRI

**Conclusion: **
**MR phase and magnitude of cell cultures was modulated by TTX administration – suggestive of neuronal currents (phase >> magnitude).**
**Future:**
**Detection in humans: pulse-sequence based neuronal frequency tuning, multivariate processing strategies, matched filters, high field.**

## Slide 37

## Section on Functional Imaging Methods

**Functional MRI Facility**

**Rasmus Birn****	****staff scientist**
**Anthony Boemio  ****	****post doc**
**Justin Edmands****	****system admin**
**Dan Handwerker****	****post doc**
**Tyler Jones ****	****post bac IRTA**
**Youn Kim ****	****	****post bac IRTA**
**Niko Kriegeskorte ****	****post doc**
**Marieke Mur ****	****student IRTA**
**Kevin Murphy ****	****post doc**
**Alissa Par****	****	****post bac IRTA**
**Vikas Patel****	****system admin**
**Dorian Van Tassell ****	****program assistant**
**Javier Castillo-Gonzalez Summer Student**
**Jason Diamond ****	****Howard Hughes Fellow**
**Thomas Gallo****	****Summer Student **
**Hauke Heekeren****	****post doc**
**David Knight****	****post doc**
**Ilana Levy****	****	****post bac IRTA**
**Marta Maieron****	****visiting fellow**
**Hanh Nguyen****	****post bac IRTA**
**Natalia Petridou****	****student IRTA**
**Douglass Ruff****	****post bac IRTA**
**Monica Smith****	****post bac IRTA**
**August Tuan****	****post bac IRTA**
**Naja Waters****	****post bac IRTA**

**Jerzy Bodurka ****	****staff scientist**
**Ellen Condon****	****technologist**
**Janet Ebron****	****technologist**
**Kenny Kan****	****	****technologist**
**Kay Kuhns****	****	****admin. lab manager**
**Wenming Luh****	****staff scientist**
**Sean Marrett****	****staff scientist**
**Marcela Montequin ****	****technologist**
**Sandra Moore****	****technologist**
**Sahra Omar****	****technologist**
**Alda Ottley****	****technologist**
**Paula Rowser****	****technologist**
**Adam Thomas****	****system admin**
**Karen Bove-Bettis****	****technologist**
**James Hoske****	****technologist**

## Interpretation

- R.M. Birn, P. A. Bandettini, The effect of stimulus duty cycle and "off" duration on BOLD response linearity. *NeuroImage*, **27, 70-82 (2005)***.*
- R. M. Birn, J. B. Diamond, M. A. Smith, P. A. Bandettini, Separating respiratory variation-related fluctuations from neuronal activity-related fluctuations in fMRI, *NeuroImage* **31, 1536-1548 (2006).**
- A. Tuan, R. M. Birn, P. A. Bandettini, G. M. Boynton, Differential transient MEG and fMRI responses to visual stimulation onset rate. **(submitted)**
- N. Kriegeskorte, J. Bodurka, and P. Bandettini, Artifactual time course correlations in echo-planar fMRI with implications for studies of brain function. **(submitted)**
- R. M. Birn, K. Murphy, P. A. Bandettini, The effect of respiration variations on independent component analysis of resting state functional connectivity. **(submitted)**
- R. M. Birn, M. A. Smith, T. B. Jones, P. A. Bandettini, The respiration response function: the temporal dynamics of fMRI signal fluctuations related to changes in respiration.** ***NeuroImage*** (in press)**

## Methodology

- R.M. Birn, R. W. Cox, P. A. Bandettini, Functional MRI experimental designs and processing strategies for studying brain activation associated with overt responses. *NeuroImage,* **23, 1046-1058 (2004)**
- K. S. St. Lawrence, J. A. Frank, P. A. Bandettini, F. Q. Ye, Noise reduction in multi-slice arterial spin tagging imaging. Magnetic Resonance in Medicine. Magn. Reson. Med. **53, 735-738 (2005).**
- N. Kriegeskorte, R. Goebel, P. Bandettini, Information-based functional brain mapping. *Proc. Nat'l. Acad. Sci. USA***, 103, 3863-3868 (2006).**
- P. A. Bandettini, Functional MRI Today, International Journal of Psychophysiology **63, 138-145 (2007) **
- J. Bodurka, F. Ye, N Petridou, K. Murphy, P. A. Bandettini, Mapping the MRI voxel volume in which thermal noise matches physiological noise – implications for fMRI. *NeuroImage,* **34, 542-549 (2007)**
- 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)**
- N. Kriegeskorte, P. Bandettini, Analyzing for information, not activation, to exploit high-resolution fMRI, *NeuroImage*,** 38, 649-662 (2007)**
- N. Kriegeskorte, P. Bandettini, Combining the tools: activation- and information-based fMRI analysis. *NeuroImage, ***38, 666-668 (2007)**

## Technology

- P. A. Bandettini, N. Petridou, J. Bodurka, Direct detection of neuronal activity with MRI: fantasy, possibility, or reality? *Applied MRI ***29 (1) pp. 65-88 (2005)***.*** **
- N. Petridou, D. Plenz, A. C. Silva, J. Bodurka, M. Loew, P. A. Bandettini, Direct Magnetic Resonance detection of neuronal electrical activity, *Proc. Nat'l. **Acad. Sci. USA*. 103, **16015-16020 (2006).**
- 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)**

## Applications

- H. R. Heekeren, S. Marrett, P. A. Bandettini, L. G. Ungerleider, A general mechanism for perceptual decision making in the human brain. Nature** 43, 859-862 (2004).**
- D. C. Knight, H. T. Nguyen, P. A. Bandettini, The role of the human amygdala in the production of conditioned fear responses. NeuroImage,** 26, 1193-1200 (2005).**
-  D. C. Knight, H. T. Nguyen, P. A. Bandettini, The role of awareness in delay and trace fear conditioning in humans. Cognitive, Affective, and Behavioral Neuroscience,** 5 (2), 158-163 (2006). **
- H. R. Heekeren, S. Marrett, D. A. Ruff, P. A. Bandettini, L. G. Ungerleider, Involvement of human left dorsolateral prefrontal cortex in perceptual decision-making is independent of response modality. Proc. Nat'l. Acad. Sci. USA,** 103, 10023-10028 (2006) **
- J. E. Dunsmoor, P. A. Bandettini, D. C. Knight, Impact of continuous versus intermittent CS-UCS pairing on human brain activation during Pavlovian fear conditioning.** **Behavioral Neuroscience,** 121, 635-642 (2007).**
- M. Maieron, G. D. Iannetti, J. Bodurka, I. Tracy, P. Bandettini, C. Porro, Functional responses in the human spinal cord during willed motor actions: evidence for side- and  rate- dependent activity. Journal of Neuroscience** 27, 4182-4190, (2007)**
- N. Kriegeskorte, M. Mur, D. Ruff, R. Kiani, J. Bodurka, H. Esteky, K. Tanaka, P. Bandettini, Matching categorical object representations in inferotemporal cortex of man and monkey.** (submitted)**

## Slide 43

## ON response amplitude: initial amp: 	1.5 times steady state ampAdaptation time constant: 		1.5sRefractory period: 		5sOFF response amplitude: 		initial amp 0.5 times steady state ampOFF response time constant: 	0.5sThe initial overshoot amplitude and decay time were chosen to roughly matchthe local field potential change measured in macaque visual cortex inresponse to rotating checkerboard, as measured by Logothetis et al. (2001).The refractory period was chosen to produce results somewhat consistent withobserved BOLD refractory period (Huettel et al., 2000).