2  Planning an fMRI study

Visual activity in the human claustrum (Coates et al. 2024)

In this section: experimenter’s decisions

  • Whole-brain or ROI analysis (or both)

  • Univariate or multivariate analysis

  • Blocked or event-related design

Analysis steps

  • Single-subject - first level - fixed effects analysis (FFX)

  • Group - second-level - random effects analysis (RFX)

This is equivalent to e.g. conducting many trials per subject to measure reaction time, and then compute a subject-specific mean per condition, after which you would perform the actual statistical inference

Multilevel modelling is also possible (for small datasets), but less frequent.

No matter what you do, your analysis will boil down to these stages.

Research questions

Whole-brain or ROI analysis?

Exploratory: Neural correlates of illusory shapes

(Larsson et al. 1999)

Hypothesis-driven: Are illusory shapes represented in the dorsal visual stream?

(Arsenovic, Ischebeck, and Zaretskaya 2022)

Defining ROIs

  • Functional localizer scan

  • Anatomical scan segmentation

  • Atlas in standard space

Functional localizer scan

Goenitzer et al., unpublished

Goenitzer et al., unpublished

Cortical atlas

HCP cortical parcellation (“Glasser atlas”) (Glasser et al. 2016)

ROI analysis is a way to deal with multiple comparison problem. But it requires an a priory and independent definition of an ROI.

There are two ways to define ROIs:

  • From an anatomical scan

  • From an additional (separate) functional experiment

Subcortical ROIs

NextBrain parcellation containing 333 anatomical structures (Casamitjana et al. 2024)

This is the state-of-the-art for anatomically-based ROI definition based on deep learning

Univariate or mutlivariate?

(Murphy, Gray, and Cook 2016)

Univariate: Does FFA respond to composite face illusion?

(Foster et al. 2021)

Multivariate: Is early visual cortex representation reflects the composite face illusion?

Goenitzer et al., unpublished

References

Arsenovic, Ana, Anja Ischebeck, and Natalia Zaretskaya. 2022. “Dissociation Between Attention-Dependent and Spatially Specific Illusory Shape Responses Within the Topographic Areas of the Posterior Parietal Cortex.” The Journal of Neuroscience, September. https://doi.org/10.1523/JNEUROSCI.0723-22.2022.
Casamitjana, Adrià, Matteo Mancini, Eleanor Robinson, Loïc Peter, Roberto Annunziata, Juri Althonayan, Shauna Crampsie, et al. 2024. “A Next-Generation, Histological Atlas of the Human Brain and Its Application to Automated Brain MRI Segmentation.” http://dx.doi.org/10.1101/2024.02.05.579016.
Coates, Adam, David Linhardt, Christian Windischberger, Anja Ischebeck, and Natalia Zaretskaya. 2024. “High-Resolution 7T fMRI Reveals the Visual Zone of the Human Claustrum.” Imaging Neuroscience 2: 1–15. https://doi.org/10.1162/imag_a_00327.
Foster, Celia, Isabelle Bülthoff, Andreas Bartels, and Mintao Zhao. 2021. “Investigating Holistic Face Processing Within and Outside of Face-Responsive Brain Regions.” NeuroImage 226 (February): 117565. https://doi.org/10.1016/j.neuroimage.2020.117565.
Glasser, Matthew F., Timothy S. Coalson, Emma C. Robinson, Carl D. Hacker, John Harwell, Essa Yacoub, Kamil Ugurbil, et al. 2016. “A Multi-Modal Parcellation of Human Cerebral Cortex.” Nature 536 (7615): 171–78. https://doi.org/10.1038/nature18933.
Larsson, Jonas, Katrin Amunts, Balázs Gulyás, Aleksandar Malikovic, Karl Zilles, and Per E. Roland. 1999. “Neuronal Correlates of Real and Illusory Contour Perception: Functional Anatomy with PET.” European Journal of Neuroscience 11 (11): 4024–36. https://doi.org/10.1046/j.1460-9568.1999.00805.x.
Murphy, Jennifer, Katie L. H. Gray, and Richard Cook. 2016. “The Composite Face Illusion.” Psychonomic Bulletin & Review 24 (2): 245–61. https://doi.org/10.3758/s13423-016-1131-5.