Bruce Fischl MGH ATHINOULA A. MARTINOS CENTER Harvard Medical School MIT CSAIL/HST some open issues in functional MRI (thanks to Larry Wald for almost.

Slides:

Advertisements

Similar presentations

BOLD Imaging at 7T Mark Elliott CfN Symposium 4/9/2008.

Advertisements

MRI Acquisition Methods for Brain Morphometry

Magnetic Resonance Imaging

MRI Phillip W Patton, Ph.D..

In Chan Song, Ph.D. Seoul National University Hospital

Richard Wise FMRI Director +44(0)

M R I Pulse Sequences Jerry Allison Ph.D..

Institute for Biomedical Engineering EXCITE Afternoon Hands-On MRI Sessions: fMRI & DTI.

MR Sequences and Techniques

Statistical Parametric Mapping

Clinical Evaluation of Fast T2-Corrected MR Spectroscopy Compared to Multi-Point 3D Dixon for Hepatic Lipid and Iron Quantification Puneet Sharma 1, Xiaodong.

Topics spatial encoding - part 2. Slice Selection  z y x 0 imaging plane    z gradient.

Basics of fMRI Preprocessing Douglas N. Greve

Comparative Analysis of Continuous Table and Fixed table Acquisition Methods: Effects on Fat Suppression and Time Efficiency for Single-Shot T2-weighted.

The Basics of MRI The Basics of MRI. Current MRI technology displays images as multiple sets of gray tone images. Visualization and interpretation of.

Wald, fMRI MR Physics Massachusetts General Hospital Athinoula A. Martinos Center MR physics and safety for fMRI Lawrence L. Wald, Ph.D.

Wald, fMRI MR Physics Massachusetts General Hospital Athinoula A. Martinos Center MR physics for fMRI Lawrence L. Wald, Ph.D.

Contrast and Acquisition

Functional Brain Signal Processing: EEG & fMRI Lesson 12 Kaushik Majumdar Indian Statistical Institute Bangalore Center M.Tech.

Terry M. Button, Ph.D. Principals of Magnetic Resonance Image Formation.

fMRI introduction Michael Firbank

Steady-state free precession and other 3D methods for high-resolution FMRI Steady-state free precession and other 3D methods for high-resolution FMRI Karla.

Multi-site Investigation of DTI Reproducibility K. G. Helmer 1, M-C. Chou 2, A. Song 3, J. Turner 4, B. Gimi 5, and S. Mori 6 1 Massachusetts General Hospital,

Psy 8960, Fall ‘06 Parallel Imaging1 SMASH and SENSE High field advantage Pros and cons … But first, review of last few homework assignments.

Psy 8960, Fall ‘06 Fieldmaps1 Fieldmaps and distortion What is a fieldmap? How can we predict distortion? How can we correct distortion?

Arterial Spin Labeling at 7T - Double Edged Sword

FMRI: Biological Basis and Experiment Design Lecture 7: Gradients and k-space FFT examples –Sampling and aliasing Gradient Gradient echo K-space

FMRI: Biological Basis and Experiment Design Lecture 12: Signal-to-Noise Ratio Things that determine signal strength –voxel size –RF coil Things that determine.

FMRI: Biological Basis and Experiment Design Lecture 8: Pulse sequences, Take 2 Gradient echo review K-space review Slice selection K-space navigation.

Psy 8960, Fall ‘06 EPI, Part 2: variants1 Segmentation Partial Fourier Spin echo vs. gradient echo Inversion recovery Long vs. short TE.

Compressed Sensing for Chemical Shift-Based Water-Fat Separation Doneva M., Bornert P., Eggers H., Mertins A., Pauly J., and Lustig M., Magnetic Resonance.

MRI Image Formation Karla Miller FMRIB Physics Group.

Parallel Imaging Reconstruction

2 High Resolution T2 Imaging Rat versus Mouse T1 MP-RAGE Dark CSF Resolution Rat: 156 x 156 x 700 µ m 3 Mouse: 138 x 117 x 400 µm 3 Coil setup: Transmit:Integrated.

B1 inhomogeneities lead to significant variations in image intensity and tissue contrast across the brain, particularly in spin echo sequences. While intensity.

Basics of Functional Magnetic Resonance Imaging. How MRI Works Put a person inside a big magnetic field Transmit radio waves into the person –These "energize"

Partial Parallel imaging (PPI) in MR for faster imaging IMA Compressed Sensing June, 2007 Acknowledgement: NIH Grants 5RO1CA and 5P41RR008079, Pierre-Francois.

Contrast Mechanism and Pulse Sequences Allen W. Song Brain Imaging and Analysis Center Duke University.

EE369C Final Project: Accelerated Flip Angle Sequences Jan 9, 2012 Jason Su.

Daily fMRI Practice John Li MD 9/27/2012. When you preparing a fMRI study, you need to Read and understand the fMRI requirements. Design and choose proper.

Contrast Mechanisms in MRI Introduction to Cardiovascular Engineering Michael Jay Schillaci, PhD Managing Director, Physicist Tuesday, September 16 th,

Recent advances in Magnetic Resonance Imaging Peter Fransson MR Research Center, Cognitive Neurophysiology Dept. of Clinical Neuroscience, Karolinska Institute.

Contrast Mechanism and Pulse Sequences

Active Detuning of Inductively Coupled Surface Coils Jolinda Smith Lewis Center for Neuroimaging University of Oregon.

Statistical Parametric Mapping

Functional Brain Signal Processing: EEG & fMRI Lesson 14

Spatial and temporal limits of fMRI Menon RS, Kim SG. Spatial and temporal limits in cognitive neuroimaging with fMRI. Trends Cogn Sci Jun;3(6):

B0 Distortion Correction in EPI Douglas N Greve MGH Martinos Center.

MRI: Contrast Mechanisms and Pulse Sequences

Magnetic Resonance Learning Objectives

Principles of MRI Physics and Engineering Allen W. Song Brain Imaging and Analysis Center Duke University.

DTI Acquisition Guide Donald Brien February 2016.

Freesurfer-based brain image analysis Csaba Anderlik UiB Csaba Anderlik UiB.

Receive Coil Arrays and Parallel Imaging for fMRI of the Human Brain

Real time shimming (RTS) for compensation of respiratory induced field changes P van Gelderen, JA de Zwart, P Starewicz, RS Hinks, JH Duyn Introduction.

Nicole Seiberlich Workshop on Novel Reconstruction Strategies in NMR and MRI 2010 Göttingen, Germany 10 September 2010 Non-Cartesian Parallel Imaging based.

Beyond the Standard EPI – New MRI Sequences available at the CBU Marta Morgado Correia MRC Cognition and Brain Sciences Unit Date.

SWIFT Dual Breast Imaging Sequence and Coil with Interleaved Adiabatic Fat Suppression high temporal and spatial resolution #3369 Computer 8 breast imaging.

Parameters which can be “optimized” Functional Contrast Image signal to noise Hemodynamic Specificity Image quality (warping, dropout) Speed Resolution.

BOLD functional MRI Magnetic properties of oxyhemoglobin and deoxyhemoglobin L. Pauling and C. Coryell, PNAS USA 22: (1936) BOLD effects in vivo.

FMRI data acquisition.

Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI at Ultra-high Field Saskia Bollmann1, Steffen Bollmann1, Alexander.

PowerGrid for harnessing high performance computing to reconstruct large sets of high-resolution non-Cartesian MRI data Brad Sutton Assoc Prof, Bioengineering.

Bioengineering 280A Principles of Biomedical Imaging Fall Quarter 2005 MRI Lecture 5 Thomas Liu, BE280A, UCSD, Fall 2005.

MRI Pulse Sequences: IR, EPI, PC, 2D and 3D

Magnetic Resonance Imaging

3T-versus-7T DTI with 36 diffusion-encoding directions at b = 3000 s/mm2 and 2.0 × 2.0 × 2.0 mm isotropic voxel resolution. 3T-versus-7T DTI with 36 diffusion-encoding.

Basics of fMRI and fMRI experiment design

Left, T1 spin-echo image at 1

Same section position with spin-echo T1-weighted sequences at 1

Presentation transcript:

Bruce Fischl MGH ATHINOULA A. MARTINOS CENTER Harvard Medical School MIT CSAIL/HST some open issues in functional MRI (thanks to Larry Wald for almost all these slides)

Integrating Function and Structure. Local functional organization of cortex is largely 2- dimensional! From (Sereno et al, 1995, Science).

Some hot topics/open questions: 1.EPI distortions. 2.Large N arrays/parallel acquisition and High field (or ultra-high field). 3.Open issues.

EPI distortions: change with TE. 3T, TE = 21, 30, 40, 50, 60ms

EPI distortions: change with slice thickness.

EPI distortions: other factors 1.Scale linearly with field strength. 2.Change with changing shim. 3.Bone/air interface particularly problematic. 4.Are inversely proportional to bandwidth.

Some hot topics/open questions: 1.EPI distortions. 2.Large N arrays/parallel acquisition and High field (or ultra-high field). 3.Open issues.

Large N Arrays 1.The sensitivity of a coil generally scales inversely with its area. 2.The sensitivity of a coil falls off with depth, with the rate of falloff inversely proportional to the coil diameter. How to get uniformly high sensitivity? Tile the head with lots of little coils!

Two ways to improve sensitivity in the brain. Big magnet Small coils

Two ways to improve sensitivity in the brain. Big magnet Small coils

MGH array development 32 ch. at 3T 90 ch. at 1.5T 32 ch. at 7T

SNR Maps – increased sensitivity everywhere 23 Channel8 ChannelCP Head Channel

Acceleration Arrays contain lots of redundant information (since each coil sees the entire brain, albeit with variable SNR) As usual in MRI, can tradeoff time and SNR – acceleration to increase EPI bandwidth and decrease distortion.

1/FOV water kyky kxkx Under-sampled kspace Increasing Bandwidth: accelerate the EPI by leaving out every other line… 1/2 FOV, from under-sampled kspace

Two ways to get to the unfolded image… FFT kspace, every other line (under-sampled) Folded, but many FFT SMASH, GRAPPA SENSE

EPI distortions: acceleration 4x acceleration at 1.5T vs. no acceleration

3D Flash with 16x accel. 1mm x 1mm x 2mm, acquisition time = 23sec Courtesy: Mathias Nittka, Siemens TR = 12 TE = 4.7 FA = 15 deg BW = 130 3T: 32 channel

What else can be done with SNR? Can also trade SNR for resolution, although the price is high!

MGH 3T 32 channel 3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 24

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 28

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 32

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 36

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 40

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 44

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 48

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 52

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 56

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 60

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel 64

3T MP-RAGE 380um x 380um x 1mm, 7 scans of 9 minutes each motion corrected TI=900ms, TR/TE/flip = 2250/4.35/9deg MGH 3T 32 channel

Single shot GRE EPI 1.0mm isotropic, 192x192, TE= 30ms R=2 GRAPPA MGH 3T 32 channel

1mm Res. Diffusion MRI iPAT=2iPAT=3 iPAT=5iPAT=4 Product EPI b = 1000 s/mm 2 256x256 matrix FoV = 256 mm Thick = 2.0 mm TR = 3200 ms TE (iPAT 2) = 112 ms TE (iPAT 3) = 94 ms TE (iPAT 4) = 87 ms TE (iPAT 5) = 87 ms Shots Courtesy Michael Zwanger & Gunnar Kruger 3T 32 channel

Courtesy: G. Sorensen and R. Wang, Thomas Benner, MGH Martinos Center 2mm isotropic DTI, whole brain, 7 minutes

7T array coil 750um isotropic resolution 7T High Resol. fMRI w/ BOSS method results from C. Miller, Univ. Oxford and C. Wiggins

1.What to do about the veins? 2.How to accurately align high res functional data to structurals? 3.Non-Fourier reconstructions to account for other distortions? 4.What to do about physiological noise? 5.How to optimally combine different echoes? Open Questions for High-Field High resolution imaging.

7 Tesla: Dielectric Resonance within head Intensity inhomogeneity in transmit B1 field (changes contrast!)

How to get rid of the veins? What is the true limit of the neural resolution of fMRI?

Larry Wald Graham Wiggins Andreas Potthast Chris Wiggins Franz Schmitt Christina Triantafyllou Gunnar Krueger Greg Sorensen Mattias Nitka Thomas Benner many others many others MGHSiemens Acknowledgements