Lecture 1 - intro

Question 1

why fMRI

Answer 1

1. non invasive measurement of brain activity
2. appealing balance between temporal resolution (seconds), spatial resolution (millimeter), and coverage (whole brain)
3. MRIs are available in many hospitals
4. inherently interdisciplinary
5. imaging analysis skills are highly sought after
6. highest end technology that is continuously evolving

Question 2

why not fMRI

Answer 2

1. indirect measure (hemodynamic (blood) response) of neural activity since it measures metabolic demands of active neurons
   -> but hemodynamic coupling is well established
2. limited spatial and temporal resolution (e.g., no single cells, no action potentials)
   -> but constant improvements, and who decides what the relevant scale is for understanding the brain
3. constrained set of experiments (e.g., head motion not possible)
   -> but many experiments are feasible and data can be combined with other techniques
4. MRI signal is noisy (low signal to noise ratios)
   -> someones noise is someones signal, constant improvements
5. analytical challenges (e.g., autocorrelations)
   -> not unique to fmri

Question 3

main components MRI scanner

Answer 3

1. main magnet: creates strong magnetic field
   -> outer circle
2. radiofrequency (RF) coil: transmits and receives radiofrequency waves
3. gradient coils: create additional magnetic fields whose strength varies along XYZ dimensions (important for localizing the signal)
   -> inner circle
4. patient table: moves patient in and out
5. computer system: controls the scanner from another room

Question 4

no net-magnetization

Answer 4

random axis
random proton phase

Question 5

what happens during longitudinal magnetization

Answer 5

axis aligned to B0 (= main magnetic field) (vertical)

random proton phase

1. Initially, the protons in your body are spinning on their own axes and are randomly oriented.
2. When placed in an MRI machine, a strong magnetic field (labeled B0) causes these protons, which act like tiny magnets, to align with the field.
3. Although they’re aligned, each proton still spins and wobbles (precession) about the direction of the magnetic field in a random phase, meaning they are not synchronized with each other.

Question 6

what happens during transverse magnetization

Answer 6

axis flipped orthogonal to B0 (= main magnetic field) (horizontal)

proton now phase aligned

protons resonate if the RF-pulse matches their precession frequency (i.e., they take on energy)

1. An MRI machine sends a radiofrequency (RF) pulse that matches the wobbling frequency of the protons.
2. When the RF pulse is applied, it knocks the protons out of their alignment with the magnetic field, causing them to flip into a new plane that is perpendicular to the B0 field (transverse plane).
3. After the RF pulse, all the protons are temporarily phase-aligned, meaning they wobble in sync, which is not their natural state.
4. This temporary alignment allows the MRI machine to detect signals from the protons as they emit energy when they attempt to return to their original alignment with the magnetic field. This emitted energy is what gives us the MRI signal that can be translated into an image.

Question 7

longitudinal relaxation (T1)

Answer 7

axis flips back into B0 direction

After RF-pulse ceases,protons emit energy in the form of RF waves that induce currents in receiver coils (That’s the MRI signal)

Question 8

transverse relaxation (T2)

Answer 8

phase coherence gets lost

After RF-pulse ceases,protons emit energy in the form of RF waves that induce currents in receiver coils (That’s the MRI signal)

Question 9

phase and precession

Answer 9

phase refers to the position of the proton spins in their precession around the main magnetic field (B0). Each proton spin precesses at a specific frequency when placed in a magnetic field, and this precession has an angular component, which is the phase. When protons are in a coherent phase, their precessional phases are aligned, leading to a stronger and more coherent signal.

Question 10

T1 weighted images

Answer 10

structural images (can distinguish different types of tissue)

high spatial resolution (~ 1mm at 3T) - low temporal resolution

high contrast, fewer artifacts

longitudinal magnitude

white matter appears lighter than gray matter

Question 11

T2 weighted images

Answer 11

functional images

lower spatial resolution (~ 2mm at 3T) - high temporal resolution

susceptible to blood oxygenation (sensitivity of images to changes in the oxygenation levels of blood within the brain)

transverse magnitude

gray matter (and cavities) appear lighter than white matter

Question 12

field strength

Answer 12

strength of the magnetic field used in MRI.

Higher Tesla values mean a stronger magnetic field, which can lead to clearer, higher-resolution images.

Question 13

slice

Answer 13

An individual 2D image of a specific layer or “slice” of the brain is acquired. This is like a single, flat picture of one level of the brain.

Question 14

volume

Answer 14

Several of these slices are combined to form a 3D representation of the brain called a volume

Question 15

voxels

Answer 15

The 3D volume is divided into tiny cubes called voxels (volume pixels). Each voxel contains data for a small part of the brain, like a tiny 3D pixel.

Question 16

proton spin

Answer 16

Protons, which are components of atomic nuclei, have a property called spin. In MRI, the spin of hydrogen protons in water molecules in the body is exploited to generate images.

Question 17

precession

Answer 17

• Precession is the motion of spinning protons as they wobble around the axis of the magnetic field. This is due to the torque of the magnetic field on the spinning protons.
• Protons resonate if the RF-pulse frequency matches their precession frequency (i.e., they take on energy).

Question 18

radiofrequency pulse

Answer 18

An RF pulse is used in MRI to perturb the alignment of the spinning protons, causing them to move out of alignment with the B0 field and produce a signal.

After RF-pulse ceases, protons emit energy in the form of RF waves that induce currents in receiver coils (That’s the MRI signal!)

Question 19

preprocessing

Answer 19

1. motion correction
2. slice time correction
3. unwarping
4. coregistration
5. normalization
6. spatial smoothing

Question 20

motion correction

Answer 20

problem:
head movements shift voxels

solution:
realignment - images are rotated and moved until they align

Question 21

unwarping

Answer 21

problem:
recorded image is often distorted

solution:
map the B0 field and correct magnetic field distortions

Question 22

slice time correction

Answer 22

problem:
Since the slices are acquired sequentially, each slice is captured at a slightly different time within the TR period.

solution:
shifting signal depending on acquisition time and then resampling at interpolated time points. this becomes more important the longer the RT (repetition time).

Question 23

coregistration

Answer 23

problem:
structural and functional images need to be aligned but differ in contrast and artifacts

solution:
maximize mutual information. aligning images with an algorithm handling different contrasts (unlike motion correction)

Question 24

normalization

Answer 24

problem:
anatomical differences between subjects - coordinates are not comparable

solution:
convert images into common space (warping all images such that they align with the same template brain)

Question 25

spatial smoothing

Answer 25

problem:
weak signals & residual anatomical differences

solution:
smoothing images suppresses noise and increases statistical power. each voxel is replaced by a gaussian-weighted average of itself and its neighbours.

Question 26

BOLD signal
(Blood Oxygenation Level Dependent) signal

Answer 26

measure detected by fMRI that indicates changes in blood oxygen levels within the brain

Question 27

Hemodynamic response function (HRF)

Answer 27

a model of the blood flow changes that occur in response to neural activity

Question 28

2 types of brain imaging

Answer 28

1. structural brain imaging: brain structure + disease/injury diagnosis
   - PET, MRI, CAT
2. functional brain imaging: study cognitive and affective processes
   - PET, fMRI, EEG, MEG

Question 29

difference MRI and fMRI

Answer 29

• MRI is structural, fMRI is functional
• MRI is 1 picture, fMRI is sequence of pictures to study change over time

Question 30

spatial resolution (low to high)

Answer 30

1. BOLD fMRI
2. MEG & EEG + PET + ASL FMRI

Question 31

temporal resolution (low to high)

Answer 31

1. MEG & EEG
2. BOLD fMRI + ASL fMRI
3. PET + ASL fMRI

Question 32

3 main goals of fMRI data analysis

Answer 32

1. localization: determine which regions of the brain are active during a task
2. connectivity: determine how different brain regions are connected
   –> Correlations across measured values across time
   –> functional. effective, and multivariate connectivity
3. prediction: use a person’s brain activity to predict their perceptions, behavior, or health status

Question 33

temporal resolution

Answer 33

• determines our ability to separate brain events in time
• in fMRI this is determined by how quickly each individual image is acquired (TR)

Question 34

spatial resolution

Answer 34

our ability to distinguish changes in an image across different spatial locations