05.06.2016 1 Max Planck Institute for Human Cognitive and Brain Sciences Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany Technical Aspects of Real-Time fMRI Nikolaus Weiskopf For Participants of OHBM Educational Course: “Real-time fMRI: Fundamental Principles for Clinical Applications” Max Planck Institute for Human Cognitive and Brain Sciences • What is Real-Time fMRI (rtfMRI)? • Applications • Technical Challenges • Prospective Motion Correction • Fast and Robust Data Acquisition • Discussion and Outlook Overview Max Planck Institute for Human Cognitive and Brain Sciences • What is Real-Time fMRI (rtfMRI)? • Applications • Technical Challenges • Prospective Motion Correction • Fast and Robust Data Acquisition • Discussion and Outlook Overview Max Planck Institute for Human Cognitive and Brain Sciences rtfMRI: Experimental Setup BOLD Processing time < Data acquistion time Cox et al., Magn. Reson. Med. 1995
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05.06.2016
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Max Planck Institute for Human Cognitive and Brain Sciences
Department of Neurophysics,Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
Technical Aspects of Real-Time fMRI
Nikolaus Weiskopf
For Participants of OHBM Educational Course:“Real-time fMRI: Fundamental Principles for Clinical Applications”
Max Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
rtfMRI: Experimental SetupBOLD
Processing time < Data acquistion time
Cox et al., Magn. Reson. Med. 1995
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Max Planck Institute for Human Cognitive and Brain Sciences Max Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
Applications of rtfMRI• Online quality assurance (QA) and subject compliance• Monitoring anaesthesia effects Wibral et al., Neuroimage 2007• Functional localizers• Piloting new paradigms• Teaching fMRI
Weiskopf et al., MRI 2007
Students in fMRI practical
Functional neuroanatomy:finger tapping
Max Planck Institute for Human Cognitive and Brain Sciences
Online Quality Assurance
Weiskopf et al., MRI 2007
EPI
Differenceand varianceimages
Head motion
Meanvariance
Backgroundnoise levelfor eachslice
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Max Planck Institute for Human Cognitive and Brain Sciences
Neurofeedback: Closing the LoopBOLD
Weiskopf et al., Neuroimage 2012Max Planck Institute for Human Cognitive and Brain Sciences
Neurofeedback: Closing the LoopBOLD
Weiskopf et al., Neuroimage 2012
Max Planck Institute for Human Cognitive and Brain Sciences
The Classic Neuroimaging Experiment
Behavior/Stimulus NeuronalActivity
Painful electric stimulus ACC BOLD activity is increased
Davis et al., J Neurophys 1997Max Planck Institute for Human Cognitive and Brain Sciences
Neurofeedback: Swapping the Variables
Behavior/Stimulus NeuronalActivity
Pain rating changes ACC BOLD activity is increased
deCharms et al., PNAS 2005
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Max Planck Institute for Human Cognitive and Brain Sciences
Neurofeedback: Swapping the Variables
Behavior/Stimulus NeuronalActivity
Pain rating changes
Weiskopf et al., Neuroimage 2012Sources: Wassermann, T. Brain Stim.; T. VarcoMax Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
rtfMRI: Timing
Processing time < Data acquistion time
Data Analysis
Image ReconstructionAcquisition Time
Max Planck Institute for Human Cognitive and Brain Sciences
Challenges of rtfMRI
• Fast processing at a high data rate• Data accumulating over time, i.e., few data/low SNR initiallyand increasing memory demand• Fast data acquisition and image reconstruction• Stability, robustness – e.g., experiment cannot be repeated• Real-time control and time stamping• Usability: on-line display, assessment of data, definition ofparadigm• Access to (raw) data on vendor‘s platform
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Max Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
Real-time Motion Correction
3D motion correction
Image time-series
- =Spurious signal change
Mathiak and Posse, MRM 2001
w/o correction
with correction
Max Planck Institute for Human Cognitive and Brain Sciences
Scanner Host Computer
Camera System
Imaging Gradients
FOV Marker pose
XPACE Libraries†
FOV realigned
*Kineticor, HI†Maclaren et al. PLOS One, 7(11), 2012
Ultrafast Prospective Motion Correction (PMC)
Gx
Gy
Gz
Max Planck Institute for Human Cognitive and Brain Sciences
Scanner Host Computer
Camera System
Imaging Gradients
FOV Marker pose
XPACE Libraries†
FOV realigned
Ultrafast Prospective Motion Correction (PMC)
Gx
Gy
Gz*Kineticor, HI†Maclaren et al. PLOS One, 7(11), 2012
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Max Planck Institute for Human Cognitive and Brain Sciences
Scanner Host Computer
Camera System
Imaging GradientsGx
Gy
Gz
FOV Marker pose
XPACE Libraries†
FOV realigned
Ultrafast Prospective Motion Correction (PMC)
*Kineticor, HI†Maclaren et al. PLOS One, 7(11), 2012
Max Planck Institute for Human Cognitive and Brain SciencesTodd et al, Neuroimage 2015
Optical Prospective Motion Correction (PMC)
Max Planck Institute for Human Cognitive and Brain Sciences
PMC detects cardio-respiratory effects
Image volume
Compliant volunteer with minimal head motion and some deliberate movement for comparison
~0.5 mm
cardiac ~3 mm~1 mm
Max Planck Institute for Human Cognitive and Brain Sciences
Motor Task and Head MotionPMC OffNo Motion PMC OnNo Motion PMC OffMotion PMC OnMotion
Displayed at p < 0.001, uncorrected Todd et al., Neuroimage 2015
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Max Planck Institute for Human Cognitive and Brain Sciences
Visual Stimulation and Head Motion
Displayed at p < 0.001, uncorrected Todd et al., Neuroimage 2015
Max Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
Optimal EPI Parameters for Maximal BOLD Sensitivity• Optimal parameters determined from field map database by modeling of susceptibility artifacts• Gains > 80%
Weiskopf et al., Neuroimage 2006Volz et al., under revisionMax Planck Institute for Human Cognitive and Brain Sciences
Multi-echo EPI: Distortion and Dropout Reduction
ORIGINAL UNDISTORTEDTE 28 ms TE 46 ms CNR-OPTIMIZED
L R
PE PEz-ShimOriginal
Dropoutin amgydalaPosse et al., Neuroimage 2003
Dropout compensation Distortion correction
Weiskopf et al., Neuroimage 2003
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Max Planck Institute for Human Cognitive and Brain Sciences
2D EPI 2D Multiband EPI 3D EPISlice excitation
~50 msper slice
~3 secpervolume
Simple iFFT
Max Planck Institute for Human Cognitive and Brain Sciences
2D EPI 2D Multiband EPI 3D EPIMulti-Slice excitation
~50 msper slice
~3 secper volume
Parallel imaging
~50 msper slice group
~1.5 secper volume
Max Planck Institute for Human Cognitive and Brain Sciences
2D EPI 2D Multiband EPI 3D EPIVolumeexcitation
~50 msper slice
~3 secper volume
~50 msper slice
~1.5 secper volume
Simple iFFT
~3 secper volume
~3 secper volume
~50 ms
Max Planck Institute for Human Cognitive and Brain Sciences
2D EPI 2D Multiband EPI 3D EPIVolumeexcitation
~50 msper slice
~3 secper volume
~50 msper slice
~1.5 secper volume
~1.5 secper volume
~1.5 secper volume
Parallel imaging
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Max Planck Institute for Human Cognitive and Brain Sciences
2D Multi-band EPI with TR from 1.1 s–6.6 s
MB 1
MB 2
MB 4
MB 6
Slice-GRAPPA Split Slice-GRAPPA
Displayed at p < 0.001, uncorrectedTodd et al., Neuroimage 2016
Max Planck Institute for Human Cognitive and Brain Sciences
2D Multi-band EPI: False Positive Activations
Slice
Phase
MB 6, Slice-GRAPPA
Simultaneously excited slices
CAIPI-shift
MB 1 MB 2 MB 4
Todd et al., Neuroimage 2016
Max Planck Institute for Human Cognitive and Brain Sciences
3D Multi-Echo EPI with Z-Shim• Multi-shot acquisition• Z-shim gradient compensates dropout• Two-directional parallel imaging allows TR ~ 1s for whole brain
Dropoutin orbito-frontalcortex
Single echo3D EPI
Dual echo3D EPIwith z-shim
tSNR
Max Planck Institute for Human Cognitive and Brain Sciences
*
-0.10
0.10.20.30.4
Visit 1 Visit 2 Visit 3 Visit 4Contr
ast E
stimate
s
NF-Training: Upregulation - Baseline
-0.20-0.100.000.100.200.30
1 2 3 4 5 6 7 8 9 10Gro
up
Comp
osite
score
Patient
Post-training Visit - Baseline Visit
Bette
r Pe
rform
ance
Example Application:SMA Training in Huntington’s Disease
Papoutsi et al., in preparation
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Max Planck Institute for Human Cognitive and Brain Sciences
Multi-Slab Echo-Volumar Imaging (EVI)
Posse et al., Neuroimage 2012
EVI (TR = 286 ms) 2D EPI (TR = 2s)
Max Planck Institute for Human Cognitive and Brain Sciences
3D EPI: Fast Acquisition Resolves Respiratory Movement, Reducing Physiological Noise
Dy, m
m/pit
ch, de
g/resp
, a.u.
Respiration belt Translation Rotation
Max Planck Institute for Human Cognitive and Brain Sciences
• What is Real-Time fMRI (rtfMRI)?• Applications• Technical Challenges• Prospective Motion Correction• Fast and Robust Data Acquisition• Discussion and Outlook
Overview
Max Planck Institute for Human Cognitive and Brain Sciences
Discussion• Main applications: neurofeedback, QA, functional localizers• Many off-line methods are available for rtfMRI• More off-line methods will become available with increasing computational power (Moore’s Law) and dedicated rtfMRI methods development (e.g., in Braintrain project).• fMRI acquisitions can be tailored to rtfMRI due to various techniques, e.g., multi-band, 3D/2D EPI.• Sampling speeds are faster than physiological noise and BOLD response – no limitation for neurofeedback any more.• PMC promises to addresses motion and physiological artifacts.
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Max Planck Institute for Human Cognitive and Brain Sciences
Outlook• Simplified access to proven advanced methods• Leverage RF coil and high field technology• Deployment in clinical trials• Better understand the effects of data quality on neurofeedback learning: speed, artifacts, SNR
Max Planck Institute for Human Cognitive and Brain Sciences
Supported by MPG, EU FP7, MRC DPFS,ERC, UCL, Horizon 2020, Siemens, Wellcome Trust
Thank you
N. Todd M. CallaghanJ. Magerkurth
O. Josephs
S. Volz
Neurophysics @ MPI-CBS
Physics @ WTCN, UCL
M. Papoutsi, G. Rees, S. Tabrizi (UCL)R. Goebel, B. Sorger (Maastricht)F. Scharnowski (Zuerich) N. Birbaumer, R. Veit (Tuebingen)C. Hutton (Siemens UK)K. Mathiak (Aachen) M. Zaitsev, M. Herbst (Freiburg)E. Yacoub, S. Moeller, E. Auerbach(Minnesota)