Experimental Design & Data Acquisition for Mapping Brain Activity (Block Design) Flashcards
What does the experimental setup consist of?
- Stimulus
- Projector
- Headphones
- Tactile stimulation, mirrors, human presence - Subject response and monitoring
- Response box, controls
- Physiological monitoring-pulse oximetry, respiration belt, skin conductance
Why is there increased BOLD sensitivity with high field?
- The magnitude of the dipole that is created – inhomogeneity increases with the magnetic field
- The susceptibility of the tissue will create a high dipole – higher inhomogeneity of the magnetic field
What is the choice of field strength for the experimental set-up?
Uusually 1.5T or 3T (but fMRI at 7T becoming established)
What are the advantages of higher field strength?
- Image SNR and BOLD CNR increase
- increased functional sensitivity - Can use higher spatial resolution
- increased functional specifity
What are the disadvantages of higher field strength?
- Increases in image artefacts (distortions, dropout)
- Increase in image noise (thermal or physiological noise)
- May restrict scanning of certain subjects/patients with metal in their body
What are the 3 different types of coils for the experimental set up?
• Volume/birdcage coils
- Standard on most MRI scanners
• Surface coils:
- Increase in sensitivity for specific regions near coil (e.g. occipital cortex)
• Phased-array/multi-channel coils
- 32 channel coil
- Multiple surface coils (e.g. currently maximum = 64), increases sensitivity throughout head
- Can use parallel imaging to speed up acquisition if available
- Increased temporal resolution
What is block design well suited to localise?
Functional areas and study steady state processes (e.g. attention)
What is block design powerful in terms of?
Detection i.e. to determine which voxels are activated
- signal strength varies with the length of the blocks
What does haemodynamic response (HR) allow ?
The rapid delivery of blood to active neuronal tissues
The brain consumes large amounts of energy but does not have a reservoir of stored energy substrates
What is cerebral blood flow essential for?
Maintenance of neurons, astrocytes and other cells of the brain
What does signal strength vary with?
Length of blocks
When does the signal not return to baseline during null-blocks decreasing the strength of the signal?
With short blocks (less than 10s)
Why does the detection power increase with high frequency alteration?
- It depends on the number of events/blocks
- The noise in the BOLD time course which occurs mainly at low frequencies
- Blocks with duration longer than the haemodynamic response reach a compromise between signal strength and noise
What is the advantage of having short blocks (<10s)
Time to have a lot of blocks
- Statistical power increases
What is the disadvantages of short blocks (<10s)?
The signal doesn’t have time to go back to the baseline
- The BOLD effect is smaller
What is the advantage of long blocks?
Large response during the task and has time to go back to baseline during rest
- High BOLD response
What is the disadvantage of having long blocks?
No time to have a lot of blocks - Statistical power decreases
- BOLD response and noise at similar frequency -> detection power smaller
What are the typical fMRI acquisition parameters
• Length of an fMRI run:
- 10-20 minutes, up to ~3 runs in a session (e.g. 200-500 volts)
• Dummy scans:
- Acquire at beginning (~4-5 volumes)
- Allow the longitudinal magnetisation to reach equilibrium
- Allow for subject to adjust to environment and noise
• Other:
- Time for training, behavioural testing, anatomical scans
What can the spatial and temporal resolution of fMRI be ultimately be limited by?
Characteristics of the physiological changes accompanying neuronal activation
Where can the BOLD signal originate?
Within and surrounding the smallest capillaries and the largest venous vessels
Where is the oxygenation changes detected?
Several mm downstream in the venous system from the site of neuronal activity
Why is mapping of the microvasculature required?
To remove signals in large vessels to optimise the spatial accuracy of fMRI
What has been performed to investigate the physical mechanism of BOLD contrast?
Theoretical modelling of the magnetic susceptibility gradients and Monte-Carlo stimulations
What is the consequence of having very low volume of blood within the brain?
Extravascular spin contribute heavily to BOLD contrast because local magnetic field gradient exist around vessels
- Remove large vessels from activation images
What is the ultimate temporal resulotion of fMRI likely to be determined by?
Physiological dynamics than the rate at which the data can be acquired
What does the BOLD signal respond to ?
neuronal activity which operates on a time scale of 1ms (synaptic transmission) to 100s of ms (information transport) is heavily lagged and damped by the haemodynamic response
What does the peak BOLD signal in activated primary cortex have?
measured latency of 5-8 seconds from stimulus onset and a similar time is required for the signal to return to a baseline upon stimulus cessation
What are the requirement for spatio-temporal?
- Volume TR [volume acquisition time]< 5s
- TE = 30 ms (at 3T)
- Spatial coverage of up to 15cm
What are main characteristic of EPI sequences?
- Rapid switching of gradients
* One excitation, one full k-space
What are limits of EPI?
- Fast k-space acquisition requires strong gradients
- Grading switching limited by peripheral nerve stimulation and gradient system (caveat heating)
- Readout times limited approximately T2* for high fidelity point-spread functions
What are functional MRI techniques deliberately sensitised to?
differences in T2* so that magnetic properties of deoxy-haemoglobin can manifest themselves as image contrast• Therefore sensitised to other sources of magnetic field inhomogeneity
What does components of inhomogeneity within imaging plan ecause?
Geometric distortion of image
What causes large scale inhomogeneity?
The magnetic susceptibility differences between air, bone and different tissue types
What causes a loss of image intensity due to spin dephasing?
Those that co-linear with slice selection direction
Why is geometric distortion particularly serious problem with EPI?
Very low frequency per point in the phase encoding direction
• Long TE = more dropout
• Long readout time = bigger distortions
When do human tissues exhibit changes in the magnetic field?
About 1-2ppm
What is another common problem with echo-planar images?
Presence of Nquist ghost