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

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 https://www.howequipmentworks.com/wp-content/uploads/2015/01/mri_seq_animation.gif

Inside the scanner https://snc2dmri.weebly.com/components--functions.html

Inside the scanner MAGNET IS ALWAYS ON (UNLESS QUENCHED)!!! http://mriquestions.com/superconductive-design.html

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

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)

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)

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

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

fMRI experiment design Event-related Easy to randomize stimuli as well as conditions Typically needs more trials than blocked design Slow (Jittered ITI = 4 -12 sec, averaged around 6 s) vs. Rapid (Jittered ITI = 2 – 4 sec, averaged around 3 sec)

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

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

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)