1. Basics of fMRI and fMRI experiment design
BCS204 Week 11.1
3/25/2019

2. How MRI scan works
Protons in water molecules align in the same or opposite direction with the magnetic field
Some with high, and some with low energy (LE)
RF pulse disturbs the alignment of LE protons
RF pulse stops; LE protons resume the original alignment
Receiver coil gets the signal

3. Inside the scanner

4. Inside the scanner MAGNET IS ALWAYS ON (UNLESS QUENCHED)!!!

5. MRI scanner at Center for Advanced Brain Imaging and Neurophysiology (CABIN)
SIEMENS PRISMA, 3 Tesla

6. A typical fMRI scan protocol
Each of the following is a pulse sequence. A series of pulse sequences is called a protocol.
Localizer (~15 s): a low resolution anatomical scan; just to locate the brain so that the following scans can be performed.
Some studies also employ a “Turbo Flash Localizer” (”TFL”) – a bit higher resolution - for studies that care about the coverage of certain regions
Anatomical scan (~4-6 mins): to get the anatomical structure of the brain
Functional scan (BOLD) (length dependent on experiment)

7. Most common parameters manipulated by experimenters in a pulse sequence
Repetition time (TR): the time between RF pulses
1 scan/shot generated per TR
Number of slices
If 42 slices, each scan/shot contains a mosaic of 42 smaller images, each of which is a slice.
Slice thickness (2-3mm)
Resolution (2 by 2 by 2mm of one voxel)

8. fMRI experiment design
Things to consider
Presentation mode of stimuli
Auditory presentation requires special consideration  scanner noise
Subject’s age
Clinical populations
Type of tasks – motion artifacts
Type of responses – special equipment needed for oral responses
Length of experiment
Inter-trial interval

9. fMRI experiment design
Typical session procedure in the scanner
Localizer
Anatomical scan
Break - Instruction
Wait for scanner to trigger the experiment
Functional scan
Fixation period as a baseline (~30 s)
Actual task

10. fMRI experiment design
Event-related
Easy to randomize stimuli as well as conditions
Typically needs more trials than blocked design
Slow (Jittered ITI = sec, averaged around 6 s) vs. Rapid (Jittered ITI = 2 – 4 sec, averaged around 3 sec)

11. fMRI experiment design
Rapid event-related
Lee et al. (2017)

12. fMRI experiment design
Slow event-related (fixed ITI)
Christidis & Reynolds (2004)

13. fMRI experiment design
Block design
Alternate “On” (experimental) and “Off” (baseline conditions)
Typically needs fewer trials than event-related design
May require more blocks of the same condition to avoid habituation: 14 stimuli of same type in a block vs. 7 stimuli of same type in a block
Christidis & Reynolds (2004)