'COVID-19 effects on olfactory function and the brain'
(AsPredicted #57511)
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1) Have any data been collected for this study already?
It's complicated. We have already collected some data but explain in Question 8 why readers may consider this a valid pre-registration nevertheless.

2) What's the main question being asked or hypothesis being tested in this study?
In this study, we invite our participants from a previous study (n=54) that was finished right before the COVID-19 outbreak in Stockholm, Sweden. That study, here referred to as Study 1, included among other things a full behavioural assessment of olfactory function, an anatomical whole-head MR T1 image, and a frontal T2 image. These three measures are again acquired in the current study. In addition, we add a 12-min long functional resting-state MR scan, which was not part of Study 1. We have asked all participants from Study 1 via email whether they have had COVID-19 and whether they have experienced problems with their sense of smell or taste, since Study 1, and invited them to participate in the current study.
We have four hypotheses:
-We hypothesize that olfactory bulb volume decreases after COVID-19 infection (directional hypothesis).
- We hypothesize that grey matter volume in olfactory cortex (anterior and posterior piriform cortex) is reduced after COVID-19 infection (directional hypothesis).
-We hypothesize that functional connectivity during rest between olfactory cortical regions (anterior and posterior piriform cortex and orbitofrontal cortex) is not affected by COVID-19.
-We hypothesize that olfactory function is decreased by COVID-19 (directional hypothesis).

3) Describe the key dependent variable(s) specifying how they will be measured.
-Olfactory bulb volume: Blinded and trained neuroradiologists will estimate the olfactory bulb volume in each MR scan.
-Grey matter volume in piriform cortex will be assessed using the standard SPM12 VBM analysis pipeline, following John Ashburner’s recommendations (https://www.fil.ion.ucl.ac.uk/~john/misc/VBMclass15.pdf).
-Resting-state functional connectivity: Data preprocessing, connectivity analysis, and group comparisons will follow those set out in Peter et al., (2021). Normal Olfactory Functional Connectivity Despite Lifelong Absence of Olfactory Experiences. Cereb Cortex. 31(1):159-168 with the exception that age and sex will not be used as covariates in the analysis due to the expected limited sample size.
-Sniffin’ sticks olfactory function test: standard calculations of TDI scores.

4) How many and which conditions will participants be assigned to?
We will split our participants into two groups: those who have had COVID-19, and those who have not. As exploratory analyses, we will also compare individuals who have had COVID-19 and olfactory dysfunction with individuals who have had COVID-19 without olfactory dysfunction.

5) Specify exactly which analyses you will conduct to examine the main question/hypothesis.
For the variables where we have pre and post measures, we will perform independent one-sided Welch’s t-tests to assess differences between groups (covid vs. controls) of changes between Study 1 and the current study. In case of null results, we will add Bayesian tests. Where only a post measure is available, we will instead perform the test directly between groups.

-Hypothesis 1: Bulb volume decreases after COVID-19 infection.
For each image, the mean value across raters and hemispheres will be used in all main analyses. (Separate results for the left and right hemispheres might be reported for completeness since this is often done in the literature).

- Hypothesis 2: Grey matter volume in olfactory cortex is reduced after COVID-19 infection.
Mean grey matter volume will be extracted from two ROIs: the anterior piriform cortex and the posterior piriform cortex, as defined in Porada et al., (2019) Multisensory Enhancement of Odor Object Processing in Primary Olfactory Cortex. Neuroscience. 2019 Oct 15;418:254–265

-Hypothesis 3: Functional connectivity between core olfactory cortical regions (anterior and posterior piriform cortex and orbitofrontal cortex) is not affected by COVID-19 infection.
We will assess resting-state functional connectivity between anterior piriform cortex, posterior piriform cortex (defined by Porada et al., (2019)), and olfactory orbitofrontal cortex (region defined by Seubert et al., (2013). Orbitofrontal Cortex and Olfactory Bulb Volume Predict Distinct Aspects of Olfactory Performance in Healthy Subjects. Cereb Cortex. 2013 Oct;23(10):2448–2456). In addition, functional connectivity between two visual regions (V1 and LOC) and two auditory regions (A1 and hAC), defined in Porada et al., (2019), will be used as a control measure with an expectation of no group differences.
-Hypothesis 4: Olfactory function is decreased by COVID-19. We will focus on the total TDI test result as well as the threshold score.

6) Describe exactly how outliers will be defined and handled, and your precise rule(s) for excluding observations.
We will exclude participants in case of excessive artifacts in the MR data impeding analysis or clinical finding in areas of interest. We will also exclude participants in the recruitment stage based on e-mail correspondence if there is too much uncertainty about whether they have been infected or not.

7) How many observations will be collected or what will determine sample size?
No need to justify decision, but be precise about exactly how the number will be determined.
Since this study is based on inviting participants from Study 1, the sample size is limited by these participants’ willingness to participate in the current study. We will include as many as possible of the 54 participants in Study 1.

8) Anything else you would like to pre-register?
(e.g., secondary analyses, variables collected for exploratory purposes, unusual analyses planned?)
At the moment of pre-registration, we have initiated data collection but the data has not been accessed.