Functional MRI

Jaewon Chung

(he/him) - NeuroData lab
Johns Hopkins University - Biomedical Engineering

icon j1c@jhu.edu
icon @j1c (Github)
icon @j1c (Twitter)

What is Magnetic Resonance Imaging (MRI)?


center

MRI Parameters

  • Repetition Time (TR): Time between successive RF pulses

  • Echo Time (TE): Time between RF pulse and signal acquisition

  • Flip Angle: Change in angle from initial alignment

    • Controlled by amplitude and duration of RF pulse
  • One machine, different sequences, different 'modalities' of images

Examples of Sequences

  1. T1-weighted (T1w): Excellent for anatomical detail.
    • brain, internal organs
  2. T2-weighted (T2w): Sensitive to fluid and inflammation.
    • cysts, tumors
  3. Gradient Echo (GRE): Sensitive to blood products.
    • blood flow, hemorrhage, iron deposition
  4. Diffusion-weighted Imaging (DWI): Sensitive to water diffusion.
    • white matter tracts

What is Functional MRI (fMRI)?

  • Idea: Blood flow increases in active brain regions.
  • Measurement: Blood Oxygenation Level Dependent (BOLD) signal
  • Caveat: fMRI measures relative changes in blood flow!

center

center

Task vs. Resting-State fMRI

  • Resting-State fMRI: Subjects are at rest, no task
  • Task fMRI: Subjects perform a task (e.g., finger tapping, watching video)

center

Relationship Between Neural Activity and Blood Flow

Lots of evidence from animals and humans!

  • Local field potentials (LFPs): measures electrical activity of nearby neurons
  • Positive correlation between LFP and BOLD signal (r > 0.5)

center

Processing fMRI Data


center

Preprocessing Steps

  • Slice time correction
    • Corrects for differences in acquisition time between slices

center

Preprocessing Steps

  • Motion Correction: Aligns all volumes (timepoints) to a reference image
    • 1st image: Reference image
    • Motion parameters: translation and rotation
    • Some volumes may be discarded.

Registration

  1. Coregistration: Aligns the fMRI to the subject's high-resolution anatomical scan.
  2. Normalization: Aligns subject's anatomical scan to standard space (e.g., MNI152 space) for group comparisons.

center

Nuisance Correction

  1. Bandpass filtering
    • Filtering out low and high frequencies
  2. Cyclical detrending
    • Removing linear and quadratic trends
  3. CompCor
    • Removing physiological noise (e.g., cardiac and respiratory signals)
    • Noise estimated from white matter and cerebrospinal fluid

What is Functional Connectivity?

Estimation

  • Apply a parcellation
  • Average BOLD signal within each region
  • Compute correlation between regions

Interpretation

  • Meaures how brain regions are temporally correlated.
  • Regions that fluctuate in together = functionally 'connected'

center

Anatomy of Functional Connectome

  • Ipsilateral: within the same hemisphere
  • Contralateral: between hemispheres
  • Homotopic: between mirror areas
  • High correlation in homotopic connections

center

Default Mode Network (DMN)

  • What is baseline state of the brain?
  • Are there consistent patterns of activity present even at rest?
  • Originally, resting state = doing nothing
  • Now, resting state = not performing a task
    • Self-referential thought: Introspection, autobiographical memory retrieval.
    • Imagining the future: Planning, simulating hypothetical scenarios.

DMN Regions

  • Medial Prefrontal Cortex (mPFC): Plays a central role in self-referential processing, thinking about one's own thoughts, emotions, and traits.
  • Posterior Cingulate Cortex (PCC) & Precuneus: Hub regions involved in diverse functions including self-related thought, memory retrieval (especially autobiographical memory), and spatial awareness.
  • Inferior Parietal Lobule (IPL): Involved in attentional shifting, integrating information from different senses, and may contribute to the embodied aspects of self-representation.

DMNs in Neurological Disorders

  • Alzheimer's disease: DMN connectivity is reduced, potentially linked to cognitive decline.
  • Depression: May show hyper-connectivity within the DMN, linked to excessive rumination.
  • Schizophrenia: Altered DMN connectivity and difficulty switching between the DMN and other task-related networks.

Other research avenues

  • Structure + function
  • Neurological and psychiatric disorders
  • Developmental trajectories

Useful Links






Questions?

- Typically interpolated to the middle slice