P2 Visual - Perception
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1 P2 Visual - Perception 2014 SOSE Neuroimaging of high-level visual functions gyula.kovacs@uni-jena.de 11/09/06
2 Functional magnetic resonance imaging (fmri) The very basics
3 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetisation Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
4 X-Ray, CT MRI
5 MRI uses a combination of Magnetic and Electromagnetic Fields NMR measures the net magnetization of atomic nuclei in the presence of magnetic fields Magnetization can be manipulated by changing the magnetic field environment (static, gradient, and RF fields) Static magnetic fields don t change (< 0.1 ppm / hr): The main field is static and (nearly) homogeneous RF (radio frequency) fields are electromagnetic fields that oscillate at radio frequencies (tens of millions of times per second) Gradient magnetic fields change gradually over space and can change quickly over time (thousands of times per second)
6 A magnet within a magnet precession
7 when placed in a magnetic field (B 0 ; e.g., our MRI machines) protons will either align with the magnetic field or orthogonal to it (process of reaching magnetic equilibrium) there is a small difference (10:1 million) in the number of protons in the low and high energy states with more in the low state leading to a net magnetization (M)
8 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetisation Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
9 Necessary Equipment 4T magnet gradient coil (inside) RF Coil Magnet Gradient Coil RF Coil Source: Joe Gati, photos
10 The Big Magnet Very strong 1 Tesla (T) = 10,000 Gauss Earth s magnetic field = 0.5 Gauss 3 Tesla = 3 x 10, = 60,000X Earth s magnetic field Continuously on Main field = B 0 RU 3T x 60,000 = B 0 Source:
11 The MRI
12 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetisation Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
13 The voxel
14 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetisation Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
15 Functional Magnetic Resonance Imaging Different from structural MRI Uses a standard MRI scanner to acquire images of functionally meaningful brain activity Typically measures changes in blood oxygenation Non-invasive, no ionizing radiation Good combination of spatial / temporal resolution Voxel sizes ~4mm Time of Repetition (TR) ~1s MRI = Magnetic Resonance Imaging (MRT (Magnetic Resonance Tomography), NMR (Nuclear Magnetic Resonance), Nuclear Spin Tomography (German: Kernspin-Tomographie))
16 Advantages and disadvantages of MRI Advantages: - non-invasive - uses endogen contrast agent (e.g. H 2 0 molecules) (though exogen contrast agents may be used in some cases) - no radiation - no known risks except with metals in use for more than 20 years - relatively high spatial resolution (~ 1 mm³) Disadvantages: - expensive ( per hour) - narrow tube - noisy - limited temporal resolution (~ 2 sec, can be reduced virtually)
17 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetization Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
18 But what about activation? MRI studies brain anatomy. Functional MRI (fmri) studies brain function. Source: Jody Culham s fmri for Dummies web site
19 BOLD Blood-Oxygenation- Level Dependent contrast
20 BOLD contrast Blood Oxyenation Level Dependent Contrast Deoxyhemoglobin - paramagnetic, oxyhemoglobin less Magnetic susceptibility of blood increases linearly with increasing de-oxygenation
21 Magnetic properties of Hemoglobine Oxygenated Hemoglobine (Hb) Deoxygenated Hemoglobin (dhb) Diamagnetic Paramagnetic Oxygenated-HGb is diamagnetic (no unpaired electron _ zero magnetic moment). Deoxygenated-HGb paramagnetic (has unpaired electrons- significant magnetic moment). Completely deoxygenated blood, has a magnetic susceptibility about 20% greater than fully oxygenated blood. (introducing an object with magnetic susceptibility causes spin de-phasing, resulting in a decay of transverse magnetization that depends on the time constant T2*). Because Blood deoxygenation affects magnetic susceptibility, MR pulse sequences sensitive to T2* show higher MR signal levels where blood is highly oxygenated.
22
23
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25 BOLD basis Increased neural firing Increased regional blood flow (overcompensating) Decrease of deoxygenated Hgb Decreased magnetic susceptibility (disturbance) of blood Increase in MRI signal intensity
26 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetization Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
27 Relative changes in cerebral blood flow following neuronal activity from Mandeville et al., 1999
28 Hemodynamic Response Function % signal change = (point baseline)/baseline usually 0.5-3% initial dip -more focal -somewhat elusive so far time to rise signal begins to rise soon after stimulus begins time to peak signal peaks 4-6 sec after stimulus begins post stimulus undershoot signal suppressed after stimulation ends
29 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetization Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
30 The indirect relationship between fmri signal and the sensory, motor, and cognitive processes.
31 Stimulus to BOLD Source: Arthurs & Boniface, 2002, Trends in Neurosciences
32 We sort of understand this (e.g., psychophysics, neurophysiology) We re clueless here! We sort of understand this (MR Physics)
33 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetization Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
34 Risks of MRI Projectile Effects: External Projectile Effects: Internal Radiofrequency Energy Gradient field changes Claustrophobia Acoustic Noise Quenching
35 The whopping strength of the magnet makes safety essential. Things fly Even big things! Source: Source: flying_objects.html Large ferromagnetic objects that were reported as having been drawn into the MR equipment include a defibrillator, a wheelchair, a respirator, ankle weights, an IV pole, a tool box, sand bags containing metal filings, a vacuum cleaner, and mop buckets. -Chaljub et al., (2001) AJR
36 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetization Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
37 fmri Experiment Stages: Prep 1) Prepare subject Consent form Safety screening Instructions 2) Shimming putting body in magnetic field makes it non-uniform adjust 3 orthogonal weak magnets to make magnetic field as homogenous as possible 3) Sagittals Take images along the midline to use to plan slices Source: Jody Culham s fmri for Dummies web site
38 fmri Experiment Stages: Anatomicals 4) Take anatomical (T1) images high-resolution images (e.g., 1x1x2.5 mm) 3D data: 3 spatial dimensions, sampled at one point in time 64 anatomical slices takes ~5 minutes Source: Jody Culham s fmri for Dummies web site
39 fmri Experiment Stages: Functionals 5) Take functional (T2*) images images are indirectly related to neural activity usually low resolution images (3x3x5 mm) all slices at one time = a volume (sometimes also called an image) sample many volumes (time points) (e.g., 1 volume every 2 seconds for 150 volumes = 300 sec = 5 minutes) 4D data: 3 spatial, 1 temporal first volume (2 sec to acquire) Source: Jody Culham s fmri for Dummies web site
40 What is fmri? What is MRI? The machine The Voxel What is fmri? The BOLD signal Hemoglobin and magnetization Hemodynamic response function Neural bases of BOLD MR safety fmri experimental steps Logic of fmri experiments
41 A typical experiment TR=2 sec (i.e. one volume takes 2 sec) 34 slices in a volume 40 images (2 Hz, 300 ms ET and 200 ms ISI) If TR=2: X 4 = 480 s, cca 500 s 250 TR (255) =8.3 min
42 Activation Statistics Functional images ~2s fmri Signal (% change) ROI Time Course Time Condition Statistical Map superimposed on anatomical MRI image Time Region of interest (ROI) ~ 5 min Source: Jody Culham s fmri for Dummies web site
43 And now we can all get some coffe/sleep!
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