Shmuel_Resting Brain

Question 1

What are the main components of an MRI scanner?

Answer 1

1. Main Coil
2. RF (radiofrequency) coil → transmit RF energy to the tissue, and secondly to receive the weak nuclear magnetic resonance signals generated by the tissue during a scan
   - 3 gradient coils (X, Y, Z) → allow spatial encoding of the MR signal

Question 2

What are the different physiological changes follow the exposure to a stimulus? (visual for ex)

Answer 2

1. Stimulus
2. Neuronal Activity
3. Change in Cerebral Blood Flow (CBF) due to neuron-vascular coupling

Question 3

What are 3 non-invasive imaging methods for the brain?
Which has the best spatial resolution?

Answer 3

MRI = Magnetic Resonance Imagine (BEST spatial resolution)
PET = Positron emission tomography
NIRS OI = Near-infrared spectroscopy optical imaging
*All measure hemodynamic changes to neuronal activity

Question 4

What are 2 methods used for intracellular recordings?

Answer 4

Minority of studies to intracellular recordings to measure transmembrane electrical events

1. Intracellular micro-electrode
2. Patch clamp
   *Need ground/reference electrode in both (always when measure potential)

Question 5

What type of recordings do the majority of electrophysiology studies use?
What are the concepts behind this?

Answer 5

Extracellular recordings
- A neuron is considered to be embedded in an extracellular medium that acts as a volume conductor (ECM has ions)

• When the membrane potential is different between 2 separate region of a neuron → flow of current in neuron occurs
  This flow is matched by return-current through extracellular path
  *If some charges move on way, opposit charges move the opposit way to equilibrate (?)

*Extracellular recording is always measured with respect to a distant neutral site (ground)

Question 6

What are the 2 components of the mean extracellular potential?

Answer 6

*Obtained by adding filter cut-off

1. MUA = Multi-Unit Activity > 400Hz
2. LFP = Local Field Potentials < 150Hz
   - Can further be classified to frequency bands used in EEG → delta (1-4Hz), theta (5-8Hz), alpha (8-13Hz), beta (12-30Hz), Gamma (30-150Hz)

Question 7

What does the Multi-Unit Activity signal/recording represent?

Answer 7

MUA is the Component of the Mean Extracellular Potential > 400Hz

Single event duration ~ 1ms
Spatial summation radius of 100-200 microns (very small)
Represents:
1. Activity of the projection neurons that form the OUTPUT of a cortical area (Action Potentials)
2. Local intra-cortical processing (very local as ~80% of synapses occur within 1-2mm of the neuron sooma)

Question 8

What does the Local Field Potential recording represent?

Answer 8

LFP is the Component of the Mean Extracellular Potential < 150Hz

Single event duration ~ 10-100 ms
Spatial summation radius of 1-2 mm (larger than MUA)
Represents:
1. Population Synaptic Potentials (EPSPs, IPSPs)
2. Voltage-gated membrane oscillations
3. INPUT to a given cortical area
3. Local intra-cortical processing (very local as ~80% of synapses occur within 1-2mm of the neuron sooma, excitatory and inhibitory neurons)

Question 9

What allows us to state that fMRI signal is an indicator of overall activity of very many neurons and processes ?

Answer 9

1. Because of the density of neuron in the cerebral cortex → 12x10^4 /mm^3

The voxel of fMRI is 2 x 2 x 2 mm^3 → there is 1 million neuron in each voxel

2. Because of the density of synpases in the cerebral cortex → 9x10^8 /mm^3
   → This means 7.2 x 10^9 synpases/ Voxel (of 2x2x2mm3)

Question 10

What is the voxel used in MRI?

Answer 10

Voxel = measurement of volume in an image
In fMRI → 2x2x2 mm^3 → about 1 million neuron/voxel

Question 11

What is the BOLD response?

Answer 11

Blood Oxygenation Level Dependent signal
→ It reflects the content of Deoxy-Hb in blood vessels
*measured by MRI signal

Question 12

What can be direct causes of a change in [Deoxy-Hb]?

Answer 12

Neuronal activity → Hemodynamic response ∆[Deoxy-Hb]

Can be due to:
- ∆ Blood Flow (CBF)
- ∆ Blood Volume (CBV)
- ∆ O2 Consumption (CMRO2)

Question 13

How is a BOLD signal measured as fMRI signal?

Answer 13

• BOLD is an indirect measure of changes in neuronal activity
• fMRI relies on magnetic properties of hemoglobin → Deoxy-Hb = para-magnetic (weak magnet, acts as contrast agent) vs Oxy-Hb = not magnetic (way too weak)

Question 14

What is the contrast agent in BOLD functional fMRI?

Answer 14

Deoxy-Hemoglobin → para-magnetic (disrupts the homogeneity of the magnetic field)
- An increase in DeoxyHb → decrease in homogeneity → decrease in BOLD signal
- A decrease in DeoxyHb → increase in homogeneity → increase in BOLD signal

*BOLD = oxygenation level

Question 15

Where does the BOLD signal originate from?
What are the control sites?

Answer 15

Originates from cortical blood vessels → control blood flow which affects the content of Deoxy-Hb in the capillaries and veins
Control sites:
1. Smooth muscles (arterioles)
2. Pericytes (processes around small vessels at the arterio-capillary junction)

Question 16

What are the X values of Deoxy-Hb and Oxy-Hb?

Answer 16

Deoxy-Hb: X ~ 1.6
Oxy-Hb: X ~ -0.3

Question 17

What are the physiological parameters influencing BOLD signal?
How do they influence it (increase/decrease)?

Answer 17

1. Increase CMRO2 → increase DeoxyHb → decrease BOLD
2. Increase CBF → decrease DeoxyHb → increase BOLD
3. Increase CBV → increase DeoxyHb → decrease BOLD

Question 18

In what order do physiological parameters influencing BOLD change?
(Start from when stimulus in shown)

Answer 18

1. Stimulus shown
2. Increased Neural activity
3. Increase oxygen consumption (initial dip)
   (neurovascular coupling)
4. 2-3 fold higher increase in CBF coming from arteries (overcompensation) → increase in CBV
5. Increased Oxy-Hb from fresh blood rushing in
6. The increase CBV takes more time to come down → increase in deoxy-Hb (little dip in BOLD)
7. Increase in MR signal / Positive Bold response

Question 19

What explains the undershoot (negative dip in BOLD signal) which follows a positive BOLD response?

Answer 19

The CBV takes time to come back down, but the there is not as much blood flow (fresh blood) so the Deoxy-Hb goes up a bit which decreases a bit the MR signal

Question 20

Which blood vessels can the BOLD signal be recorded from?

Answer 20

• Capillaries (gas exchange)
• Venules and veins (drain deoxy-Hb)

*Not arteries and arteriols as they do not carry deoxy-Hb

Question 21

How can optical imagin be used in a similar way as fMRI?
*To measure Intrinsic signals

Answer 21

*Another way to measure BOLD signal

• Relies on absorption of 605 nm by deoxy-Hb (being much greater than absorption of 605nm by Oxy-Hb)

At baseline → 50/50 deoxy/oxy → ∆R/R = 0
Initial dip → more deoxy-Hb than Oxy-Hb → ∆R/R < 0 because more light is absorbed and less is reflected back to the camera
Positive BOLD → more OxyRBC from blood rushing (increase in CBF) → less absorption and more reflection of the light back to the camera → ∆R/R > 0

Question 22

What are Voltage sensitive dyes ?
How does imaging work?

Answer 22

Voltage sensitive dyes have a portion inside the cell and a portion outside the cell membrane

Voltage-senstiive dyes change their fluorescence in response to voltage changes
- Changes in neuronal activity → changes in membrane potential → changes in fluorescence
- Capable of providing linear measurements of firing activity of single neurons or large neuronal populations

Mechanism:
1. Shine 630nm excitation light
2. Fluorophore are excited and emit light back
3. This light encounters 665nm dichroic mirror (wv > 665nm go straight to Ultima camera // wv < 665nm are deflected to Dalsa camera)

Question 23

What is the timing between BOLD signal and neurophysiological response?
What data did they compare to assess this lag?

Answer 23

BOLD signal lags behind the neurophysiological response

Voltage-Sensitive dyes vs BOLD (optical imaging)

Question 24

How did they answer the following question: Is there a quantitative relationship between the BOLD signal and the firing rate? (How much does the BOLD signal change for 1 AP?)

Answer 24

Compared the positive BOLD response in human V1 exposed to grating stimuli vs Average firing rates in monkey V1 in response to the same stimuli

Conclusion: Positive BOLD responses in human V1 are proportional to AVERAGE FIRING RATES in monkey V1

*Also CBF vs LFPs in the cerebellar

This raises the question: Is the BOLD signal caused by spiking activity? (NO, but it is correlated)

Question 25

What did they see when they compared Cerebellar blood flow vs LFPs? What conclusions were pulled from this experiment?

Answer 25

1. Electrically stimulated the climbing fibers or the parallel fibers in the cerebellum 2. Measured CBF Results: Linear increase relationship between the changes in LFP and the increase in %CBF in climbing fibre stimulation Sigmoidal relationship between the changes in LFP and the increase in %CBF in parallel fibre stimulation Conclusion: 1. The hemodynamic response (BOLD) increases monotonically with increasing neurons responses *Time course will never go down until the end of the stimulus 2. The hemodynamic response is in many instances ~ linear (proportional) with the underlying neuronal spike activity 3. Non-linearities between the hemodynamic response and nuerophysiological activity have been observed (ex: parallel fibres of cerebellum)

Question 26

Which type of neuronal activity causes BOLD responses: spikes or synaptic activity? How can we find out?

Answer 26

*Use cerebellar properties to dissociate spiking activity vs synaptic activity Look at divergence of spike rate and blood flow during parallel fibre stimulation 1. Record activity from purkinje cells 2. Stimulate parallel fibers which inhibit the purkinje APs 3. Still see increase in BOLD signal (even in firing of inhibitory neurons) Activity-dependent CBF increases evoked by stimulation of cerebellar parallel fibres are dependent on synaptic excitation (including excitation of inhibitory inter-neurons) - Net activity of Purkinje cells in unimportant for the vasculature response (purkinje cells are principal excitatory neurons of cerebellar cortex) CONCLUSION: Cerebellar Blood Flow does NOT depend on spiking activity

Question 27

What physiological response/neural activity does the BOLD response reflect exactly? What are important aspects to take into account?

Answer 27

1. BOLD response reflects a local increase in neural activity assessed by the mean Extracellular Field Potential signal 2. BOLD response reflects changes in LFP/synaptic activity /input to- and local processing in a region - Not MUA/output of a region (APs) *Dissociation of MUA and BOLD-signal → In long stimulus exposure, the MUA showed spike at the start and decreased whereas the BOLD response was higher during the whole duration of stimulus (just delayed a bit) Signal to Noise Ratio (SNR) of the neural signals is much higher than that of the BOLD fMRI signal → Thresholding methods are likely

Question 28

What was observed when looking at the Signal to Noise Ratio of BOLD vs Neural signal?

Answer 28

*Measured amplitude in units of standard deviation Neural response to a stimulus showed ~60 SD units increase in neural response BOLD response to this stimulus showed a delayed ~ 2 SD units increase in BOLD signal Conclusion: SNR of the neural signals is much higher than that of the BOLD fMRI signal → Thresholding methods are likely to underestimate a great deal of actual neural activity related to the stimulus or task

Question 29

What are the frequencies of spontaneous fluctuations in resting state networks?

Answer 29

SLOW termporal scale → 0.01 Hz - 0.1 Hz (1 cycle = 10s - 100s) Large amplitude fluctuations in spontaneous fMRI signals in the resting state in human cerebral cortex

Question 30

What is functional connectivity in the resting state?

Answer 30

Functional connectivity corresponds to 2 areas which have correlated function fMRI signals at rest Analysis is based on Pearson's correlation (-1 <= r <= 1) → coefficient estimates similarity of time-courses of signals Areas that are functionally connected in resting state are called RESTING STATE NETWORKS

Question 31

What is anatomical/structral connectivity vs functional connectivity?

Answer 31

Structural connectivity = axonal projections from 1 area (A) to another (B) *Inject tracer and follow the signal Functional connectivity = statistical dependent (ex: correlation) between the time-courses of activities in areas A and B *2 areas that show functional connectivity are not necessarily anatomically connected

Question 32

How many resting networks are known in the human brain? What are they?

Answer 32

10 different resting state networks: - Medial visual - Occipital pole visual - Lateral visual - Default mode network - Cerebellum - Sensory-motor - Auditory - Executive control - Fronto-parietal (perception-somesthesis-pain) - Fronto-parietal (language cognition)

Question 33

What is the Talairach system?

Answer 33

*Stereotactic coordinates - Talairach coordinate system is defined by rotating the brain such that the anterior and posterior commissures crossings with the mid-sagittal place from a horizontal line - Distances are measured from the anterior commissure which is defined as the origin of the Talairach coordinate system (0,0,0) - This coordinate system makes it possible to spatially scale or wrap an individual brian MRI image onto a model prototypical brain *This model prototypical brain is made by averaging many Talairach brain models

Question 34

What are the 2 columns/different planes of each resting state networks? What is BrainMap?

Answer 34

Left column = RSN → 36 subject resting fMRI dataset Right column = BM → 26,671-subject BrainMap activation database - a corresponding network from BrainMap, shown superimposed on the MNI152 standard space template image - 3 most informative orthogonal slices - Networks were compared by computing spatial cross-correlation: mean correlation = 0.53 BrainMap = database of brain coordinates that are activated by specific tasks *in Talairach coordinates to be able to compare

Question 35

What is the spatial cross-correlation value between the resting state functional networks and the active state of that same network?

Answer 35

r = 0.53 → these 2 networks are related *Brain functional networks during resting state and activation do overlap

Question 36

What is the default mode network? What experiment allowed to observe these regions?

Answer 36

The Default mode network on of the multiple resting state networks Regions of the brain regularly observed to DECREASE their activity during attention compared to active state *a set of regions more active during passive tasks than tasks demanding focused external attention Meta-analysis of 9 functional PET brain imaging studies. In each of the studies included, the subjects processed a particular visual image in the task state and viewed it passively in the control state → decreased activity (blood flow) in task state

Question 37

What is the PCC?

Answer 37

PCC = posterior cingulate cortex, a central part of the default mode network There is an intrinsic correlation between a seed region in the PCC and all other voxels in the brain part of the default mode network *We decided to set a seed in PCC because we know it is in the default mode network so use as a reference site Anti-correlated activity with IPS as IPS is part of the dorsal attention networks → anti-correlation during resting and active state Conclusion: the brain is intrinsically organized into dynamic, anti-correlated functional networks

Question 38

Which 2 functional networks are anti-correlated in the brain? What does it show?

Answer 38

The default mode network and the dorsal attention network show decreases and increases, respectively, during tasks; they also show anti-correlated spontaneous fluctuations. Conclusion: the brain is intrinsically organized into dynamic, anti-correlated functional networks

Question 39

What are some hypotheses about the function of Default Mode Network? What studies support these hypotheses?

Answer 39

1. Supports self referential processes 2. Introspection 3. Supports mentalizing, reminiscence and imagination to fill the social void in loneliness 4. Ongoing processes surrounding consciousness and awareness These hypotheses are supported by studies that show that: - Default Mode Network altered activity during sleep - Altered DMN activity in Mild Cognitive Impairment (MCI), Alzheimer's disease (AD), Schizophrenia, Depression

Question 40

What are hypotheses on the functional role of spontaneous activity and resting-state networks in the brain?

Answer 40

- Involvement in functionally relevant information processing - A non-random, coordinated interaction of ongoing and evoked activity in perception and behaviour - Scanning of context possibilities, making it easier to lock on a concurrent ‘scene’ or stimulus - Maintenance and enfrocement of synapses as part of transforming short term to long term memory Could be used to: - Analyze the pattern of connecitons between areas in the healthy human brain - Contribute to diagnosing neurlogical and psychiatric conditions - Potentially, for serving as bio-markers for progession of diseases and for testing efficacy of drugs (can they restore an altered resting-state network?)

Question 41

What methods allow to study resting-state networks at the macro-scale?

Answer 41

- Slow-fluctuations in the BOLD fMRI signal → mostly reflects fluctations in neurophysiological activity - Similarity of time-courses of slow-fluctuations in EEG, MEG, NIRS (Near-Infra-Red-Spectroscopy) optical imaging signals too → fMRI shows the best spatial resolution for defining the networks *CNS = 1m Larg scale networks = 10 cm

Question 42

What are the different scales at which brain networks can be studied?

Answer 42

1. Microscopic → Single neurons and their synaptic connections (anatomical connections by diffusion MRI) 2. Mesoscopic → Connections within and between cortical columns or other type of local cells assemblies (~ mm) 3. macroscopic → Anatomically segregated brain regions and inter-regional pathways *IMPORTANT: Resting-state netowrks are a multi scale phenomenon

Question 43

Can we measure resting-state networks at the mesoscale with fMRI and the ms time-resolution scale with fMRI?

Answer 43

NO - Conventional fMRI voxel is 2 x 2 x 2 mm - Conventioanl fMRI sampling rate is one volume/1s - BOLD signal is sluggish (peaks at 5-6s delay) - With fMRI alone, we possibly miss fine-scale information in space and time

Question 44

What experimental method can be used to measure resting-state networks at the mesoscale ? What was seen when just looking at spontaneous activity this way?

Answer 44

Optical imaging using Votlage-Sentitive Dyes → capable of providing linear measurements of firing activity of single neurons, or large neuronal populations with a milli-sec time resolution scale *Combined with intracellular recording in the case seen in class Result of spontaneous activity: - Intracellular peaks in potential correlated with APs - Increase in field potentials (voltage sensitive dyes) around the neuron of interest correlated strongly with APs and intracellular depolarizations Pearson's correlation = 0.9

Question 45

Describe the experiments done to assess if the ongoing activity (spontaneous) reflects the brain's fuctiona networks also at the meso-scale. Do activity patterns corresponding to orientation maps occur spontaneously more than is expected by chance?

Answer 45

1. Look at active responses to different orientation gratings in task state (anesthetized animals) 2. Look at spontaneous activity patterns as see if they correlate with the response to horizontal gratings (in this case) - Spontaneous activity is obtained by showing a unifrm gray image to the animal Conclusion: Cotical activity patterns that are similar to the pattern of response to oriented gratings occur spontaneously more than is expected by chance (~15-20% of the time) - These pattern may span a large area (up to 4 x 6 mm)

Question 46

What control was used in the experiment showing that spontaneous activity correlates with orientation grating responses?

Answer 46

The "control" distribution was obtained by inverting the referece (evoked) map upside down → 0 correlation

Question 47

How is spiking activity of a single horizontally tuned neuron correlate with spontaneous activity around it?

Answer 47

A neurin has a preferred pattern of cortical activity, that corresponds to the pattern of population activity obtained by stimulating with the neuron's optimal orientation stimlus The neuron is more likely to fire when this pattern emerges (the multi-neuron response resembles the response to horizontal grating) regardless of stimulation, or not (spontaneous horizontal-like pattern)