From e2d3523243edd00d2427b12f5bfacf69a0fb0021 Mon Sep 17 00:00:00 2001 From: henryy152 Date: Wed, 15 Jul 2026 17:05:56 +0200 Subject: [PATCH] Update skeleton.Rmd new fmri template --- .../fmri_v2_prereg/skeleton/skeleton.Rmd | 388 ++++++++++++++++++ 1 file changed, 388 insertions(+) diff --git a/inst/rmarkdown/templates/fmri_v2_prereg/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/fmri_v2_prereg/skeleton/skeleton.Rmd index fbf2ac4..abed9ee 100644 --- a/inst/rmarkdown/templates/fmri_v2_prereg/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/fmri_v2_prereg/skeleton/skeleton.Rmd @@ -37,6 +37,394 @@ Enter your response here. Be as specific as possible about your regions of interest (ROI) and definitions of other relevant variables mentioned here. How to define your ROIs or operationalize these relevant variables should be detailed in the section Variables and Analysis Plan. --> +Enter your response here. + +| **Hypotheses** | **Checklist** | +| ----------- | ----------- | +| Is the hypothesis directional or non-directional? | ___ | +| If directional, state the directional relationship between your (manipulated or measured) variables. | ___ or NA | +| For interaction effects, describe the expected shape of the interactions. | ___ or NA | +| If you are manipulating a variable, formulate predictions for successful manipulation checks: what variables will you use to check whether your manipulation worked? If not, explain why no manipulation check is included. | ___ or NA | +| A figure or table with expected results, e.g., to describe complex interactions. | ___ or NA | +| If multiple alternative predictions can be made for the same IV-DV combination, describe what outcome would be predicted by which theory. | ___ or NA | + + + + +# Design Plan + + +## Study Type* + + +- Experiment (incl. a manipulation or treatment to which participants are randomly assigned) +- Observational study (data collected from subjects without having been randomly assigned to a treatment) +- Other: ____________________ + + +## Study Design* + + +Enter your response here. + +**Experiment / Intervention study** + +| **Experiment / Intervention study** | **Checklist** | +| ----------- | ----------- | +| Are effects of an intervention tested in one population by allocating participants randomly to the experimental or control group and testing pre and post intervention? (randomized controlled study) | ___ or NA | +| Are participants allocated to only one group or re-allocated to the other group after a wash-out period? (crossover study) | ___ or NA | +| Are intervention effects tested in different populations? (e.g., patients vs. controls) | ___ or NA | + +**Observational study** + +| **Observational study** | **Checklist** | +| ----------- | ----------- | +| Case-control study (e.g. patients vs. healthy controls) | ___ or NA | +| Classical fMRI study (e.g. healthy participants performing the same task) | ___ or NA | +| Cross-sectional study (e.g. differences in fMRI activity predict between-person differences in a trait) | ___ or NA | +| Cohort study/longitudinal study (e.g. fMRI or change in fMRI predict within-person change in a trait) | ___ or NA | + + +## Experimental design* + + +Enter your response here. + +**Design specification** + +| **Design specification** | **Checklist** | +| ----------- | ----------- | +| Design type (task, rest; event-related, block, mixed design, naturalistic) | ___ | +| Instructions to subjects (what were they asked to do?) | ___ | +| State whether or not participants practiced the task, and if so, describe the practice. | ___ | +| Conditions & Stimuli (as detailed as possible, pictures encouraged) | ___ | +| Number of runs, blocks, trials or experimental units per session and/or subject | ___ | +| Timing and Duration (length of each trial and interval between trials, jitter) | ___ | +| Was the design optimized for efficiency? If so, how? | ___ or NA | +| Randomization/pseudo-randomized/counterbalancing (why/why not done & how) | ___ or NA | +| Length of experiment (length of full scan and each run) | ___ | +| Run order (of tasks within scanner) | ___ or NA | +| Presentation software & response collection (software and hardware, name, version, operating system; code if possible) | ___ | + +**Piloting** + +| **Piloting** | **Checklist** | +| ----------- | ----------- | +| Did you validate your stimuli? (If yes, describe study & results) | ___ or NA | +| Did you pilot your study design? (If yes, describe study and results) | ___ or NA | + + + + +## Blinding* + + +| **Blinding** | **Checklist** | +| ----------- | ----------- | +| No blinding is involved in this study. | ___ or NA | +| For studies that involve human subjects, they will not know the treatment group to which they have been assigned. | ___ or NA | +| Personnel who interact directly with the study subjects (either human or non-human subjects) will not be aware of the assigned treatments. (Commonly known as "double blind") | ___ or NA | +| Personnel who analyze the data collected from the study are not aware of the treatment applied to any given group. | ___ or NA | +| Additional blinding in this study: ______________________ | ___ or NA | + + +## Randomization* + + +Enter your response here. + + +# Sampling Plan + + +## Details of Larger Project* + +**Is your preregistration part of a larger project?** + +- Yes +- No + + + +Enter your response here. + + +## Existing data* + + +- Registration prior to creation of data +- Registration prior to accessing the data +- Registration prior to any human observation of the data +- Registration prior to analysis of the data +- Registration following analysis of the data + + +## Explanation of Existing Data + + +Enter your response here. + + +## Data collection* + + +- **No.** There is no need to describe the data collection in complete detail in your preregistration. Nonetheless, it is strongly recommended to include information on your sample (see checklist below) and behavioral/fMRI data acquisition in a short paragraph as it would appear in the Methods section of a publication. Especially mention details important for your choices in Variables and Analysis Plan (e.g. temporal/spatial resolution of fMRI which may motivate certain preprocessing or analysis procedures). +- **Yes.** Describe all steps of data collection including your sample description (see checklist below). Make sure to detail procedures of all relevant behavioral and fMRI data acquisition steps. Other measurements relevant to address your hypotheses or that are included for different purposes (e.g., characterizing groups, sensitivity analysis, exploratory analysis) may also be detailed here. + +Enter your response here. + +**Sample description** + +| **Sample description** | **Checklist** | +| ----------- | ----------- | +| Population | ___ | +| Recruitment efforts | ___ | +| Inclusion criteria | ___ | +| Exclusion criteria | ___ | +| Reimbursement for participation | ___ | +| Information on ethics approval and informed consent | ___ | +| Number of participants tested and analyzed | ___ | +| Age | ___ | +| Sex / Gender | ___ | +| Handedness | ___ | +| Clinical criteria | ___ or NA | +| Matching strategy | ___ or NA | +| Other relevant participant or group characteristics for your study | ___ or NA | +| Study timeline including all measures | ___ | + + + + +## Other Measures + + +Enter your response here. + + +## Sample Size* + + +Enter your response here. + +**Justification of sample size or stopping rule** + +| **Justification of sample size or stopping rule** | **Checklist** | +| ----------- | ----------- | +| Power analysis for fMRI or behavioral analysis. Please provide all details on your calculation. (Strongly recommended; no standard procedures for fMRI power analysis exist, but see https://brainpower.readthedocs.io/en/latest/index.html for available tools.) | ___ or NA | +| Time constraints (e.g., will recruit for one year or until X date) | ___ or NA | +| Money constraints (e.g., monetary support will support up to X subjects) | ___ or NA | +| Personnel constraints (e.g., will recruit for time period in which personnel support is available) | ___ or NA | +| Other: ___________________ | ___ | + + + +Enter your response here. + + +# Variables + + +## Manipulated variables + + +Enter your response here. + + +## Measured variables* + +**Behavioral data** + + +| **Measured variables** | **Checklist** | +| ----------- | ----------- | +| Outcome measures/dependent variables (specify whether confirmatory or exploratory outcome, how variable was measured, scale/range of measure, which subscale/component of measure you will use). | ___ | +| Predictor measures/independent variables (specific measure, scale/range of measure, which subscale/component of measure you will use). | ___ | +| Covariate measures (specific measure, scale/range of measure, which subscale/component of measure you will use). | ___ or NA | + +**Quality control** + +| **Quality control** | **Checklist** | +| ----------- | ----------- | +| Any outcome-neutral criteria that must be met for successful testing of the stated hypotheses (e.g., absence of floor or ceiling effects, positive controls, or other checks orthogonal to the experimental hypotheses). | ___ | +| How will you determine which subjects, data points or measures (if any) to exclude from your analyses? If possible, specify objective exclusion criteria (due to technical errors, slow reactions, instructions not understood, accuracy below a certain threshold, or for any other reasons). | ___ or NA | +| How will you deal with incomplete or missing data (e.g., missing timepoints or missing/incomplete data within or between runs; what percent missing will be included)? Under what conditions would data be replaced and how? | ___ or NA | +| If possible, define contingency plans for such cases (e.g., plans if x% of behavioral data is missing; if a questionnaire is missing for more than 10% of participants it will not be used, or will be replaced by another questionnaire if it does not show sufficient variability). | ___ or NA | + +**Transformations** + + + +Enter your response here. + +Code, if applicable: link to shared code for scoring behavioral data. +```{r scoring behavioral data, include = TRUE} + +``` + +**fMRI data** + + +Enter your response here. + +**Quality control** + +| **Quality control (fMRI)** | **Checklist** | +| ----------- | ----------- | +| Incidental findings (protocol for review of any incidental findings, and how they are handled, in particular with respect to possible exclusion of a subject's data). | ___ or NA | +| Motion monitoring (for functional acquisitions, any visual or qualitative checks for severe motion; likewise, for structural images, checks on motion or general image quality). Including prospective quantitative motion monitoring and/or correction? | ___ | +| How will you determine which data points or samples (if any) to exclude from your analyses? How will outliers be defined and handled? If possible, specify objective exclusion criteria, e.g. a participant has X percentage of volumes with motion or exceeds a pre-defined motion threshold, or general artifacts qualitatively/quantitatively defined (multiband stripes, respiration-related, registration failure due to atrophy/lesion, etc.). | ___ | +| How will you deal with incomplete or missing data (e.g., missing timepoints or missing/incomplete data within or between runs; what percent missing will be included)? Under what conditions would data be replaced? | ___ or NA | +| Other quantitative quality control metrics (signal-to-noise ratio, contrast-to-noise ratio, motion parameters, outliers, etc.)? How will these be assessed (software, version)? Will any factor into the decision to exclude subjects, and if so, how? | ___ or NA | + +**Anatomical preprocessing** + +| **Anatomical preprocessing** | **Checklist** | +| ----------- | ----------- | +| Intensity non-uniformity correction | ___ or NA | +| Brain extraction | ___ or NA | +| Tissue segmentation | ___ or NA | + +**Functional preprocessing** + +| **Functional preprocessing** | **Checklist** | +| ----------- | ----------- | +| Remove first volumes to reach steady-state (during acquisition or preprocessing)? How many volumes were discarded? | ___ or NA | +| Distortion correction (fieldmap, ap-pa acquisitions) | ___ or NA | +| Intensity normalization | ___ or NA | +| Slice timing correction (specify reference slice, e.g., first slice, and interpolation, e.g., Fourier phase shift interpolation) | ___ or NA | +| Primary motion correction / realignment (reference scan, image similarity metric, type of interpolation, degrees-of-freedom and optimization method) | ___ or NA | +| Intrasubject registration (e.g. anatomical to functional) | ___ or NA | +| Directionality (e.g. anatomical to functional, functional session 1 to session 2, etc.) | ___ or NA | +| Transformation model (linear or nonlinear) | ___ or NA | +| Degrees of freedom | ___ or NA | +| Interpolation method | ___ or NA | +| Image similarity metric | ___ or NA | +| Intersubject registration (e.g. anatomical/functional to template) | ___ or NA | +| Brain image template space, name, modality and resolution (e.g., MNI Avg152, T1 2 × 2 × 2 mm; customized sample template) | ___ or NA | +| Directionality (e.g. anatomical to functional, functional session 1 to session 2, etc.) | ___ or NA | +| Transformation model (linear or nonlinear) | ___ or NA | +| Degrees of freedom | ___ or NA | +| Interpolation method | ___ or NA | +| Image similarity metric | ___ or NA | +| Smoothing: size and type of kernel (provide justification for size) | ___ or NA | +| Temporal filtering (type of filter, frequency band) | ___ or NA | + + + +Code, if applicable: link to shared code for preprocessing data. +```{r preprocessing fMRI data, include = TRUE} + +``` + + +# Analysis Plan + + +## Statistical modeling* + +**Behavioral analysis** + + +| **Behavioral analysis** | **Checklist** | +| ----------- | ----------- | +| Statistical model (e.g., ANOVA, multiple regression, etc.) and its specification (each variable included as predictor/factor, incl. its levels, outcome, or covariate). | ___ | +| Specify any interactions that will be tested. | ___ or NA | +| Name assumptions that need to be met and how they will be tested. | ___ | +| Include a contingency plan in case assumptions are not met. | ___ | +| Include software and packages used for each test. | ___ | +| What criteria will you use to make inferences? (e.g. p-values, Bayes factors, specific model fit indices, incl. cut-off criterion where appropriate). | ___ | +| Note whether you will adjust for multiple comparisons and how (e.g. correction procedure, number of tests included), or explain why not. | ___ | + +**fMRI analysis** + + +Enter your response here. + +**Individual (first) level modeling** + +| **Individual (first) level modeling** | **Checklist** | +| ----------- | ----------- | +| Event-related predictors (modeled duration (or zero), whether parametric modulation is used) | ___ or NA | +| Block design predictors (note whether or not baseline will be explicitly modeled) | ___ or NA | +| Include design matrix and efficiency/collinearity measure (recommended) | ___ or NA | +| HRF basis (e.g. canonical only, canonical with temporal derivative, or with temporal and dispersion derivative, Finite Impulse Response model) | ___ | +| Movement regressors; specify if squares and/or temporal derivative used. | ___ | +| Any other nuisance regressors, and whether they were entered as interactions (e.g. with a task effect in 1st level fMRI, or with group effect). | ___ | +| Any orthogonalization of regressors or parametric modulators, and set of other regressors used to orthogonalize against. | ___ or NA | +| Contrast construction (exactly what terms are subtracted from what? Define these in terms of task or stimulus conditions instead of underlying psychological concepts). | ___ | +| Model settings: for mass-univariate first level fMRI, these include drift regressors (e.g. DCT basis in SPM, with specified cutoff) and autocorrelation model (e.g., global approximate AR(1) in SPM; locally regularized autocorrelation function in FSL). Check your imaging toolbox for default settings. | ___ | + +**Group (second) level modeling** + +| **Group (second) level modeling** | **Checklist** | +| ----------- | ----------- | +| State and justify statistical model and estimation method, inference type (mixed/random effects or fixed), e.g., "Mixed effects inference with one sample t-test on summary statistic" (SPM), or "Mixed effects inference with Bayesian 2-level model with fast approximation to posterior probability of activation" (FSL). | ___ | +| If more than 2 levels, describe the levels and assumptions of the model (e.g., are variances assumed equal between groups). | ___ or NA | +| If multiple measurements per subject, list method to account for within-subject correlation, exact assumptions made about correlation/variance. | ___ or NA | +| For group model with repeated measures, specify how condition effects are modeled (e.g. as factors, or as linear trends), and whether subject effects are modeled. | ___ or NA | +| For group effects: clearly state whether or not covariates are split by group (i.e. fit as a group-by-covariate interaction). | ___ or NA | +| Model type (e.g., Mass Univariate, Multivariate (e.g. ICA on whole brain data), Local Multivariate (e.g. "searchlight"), Representational Similarity Analysis, psychophysiological interaction (PPI)). | ___ | +| Model settings (e.g. for mass-univariate group level fMRI: fixed effects vs. random/mixed effects model (OLS, weighted least squares/FLAME, global weighted least squares/MFX); any specific variance structure; for local multivariate: number of voxels in the local model and model used, e.g. Canonical Correlation Analysis, with any constraints). | ___ | + +**ROI analysis** + +| **ROI analysis** | **Checklist** | +| ----------- | ----------- | +| Will you limit your analysis to a specific ROI? (e.g. unilateral, cerebellum) | ___ or NA | +| How will you define your ROI (e.g., functional, anatomical, meta-analysis, parcel localizer)? | ___ or NA | +| Justify definition of ROI and analysis conducted with it (e.g., if your ROI is defined based on the cluster, how will you ensure your ROI analyses are not circular?). | ___ or NA | +| How was signal extracted within ROI? (e.g., average parameter estimates, FIR deconvolution?) | ___ or NA | +| If percent signal change reported, how was scaling factor determined (e.g., height of block regressor or height of isolated event regressor)? | ___ or NA | + +**Inference on statistic image (thresholding)** + +| **Inference on statistic image (thresholding)** | **Checklist** | +| ----------- | ----------- | +| Whole brain or a specific search region? Specify type of search region analysis, and the volume in voxels or mm³. | ___ | +| If not whole brain, state how the region will be determined (method for constructing region should be independent of present statistic image). Carefully describe any small volume (SV) correction used for each contrast, incl. named anatomical regions from a publicly available ROI atlas (if anatomically defined) or the functional task and risk of circularity (if functionally defined). All SV corrections should be fully described in the methods section, not just mentioned in passing in the results. | ___ or NA | +| Statistical type, e.g., voxel-wise (aka peak-wise in SPM) or cluster-wise (cluster size, cluster mass, threshold-free Cluster Enhancement/TFCE). | ___ | +| Statistical threshold used to infer significance (e.g. p < 0.05) | ___ or NA | +| If cluster-wise (cluster size or mass) significance, state cluster-defining threshold (e.g., p = 0.001), and for all cluster-wise methods report the neighborhood size used to form clusters (e.g. 6, 18 or 26). | ___ or NA | +| For TFCE, report use of non-default TFCE parameters. | ___ or NA | +| P value computation. Report if anything but standard parametric inference was used to obtain (uncorrected) p-values. If a nonparametric method was used, report the method (e.g. permutation or bootstrap) and number of permutations/samples used. | ___ | +| Multiple test correction. Specify the type of correction and how it is obtained, e.g., Familywise Error (Random Field Theory, Permutation, Monte Carlo, Bonferroni), False Discovery Rate (Benjamini & Hochberg FDR, Positive FDR, Local FDR, Cluster-level FDR), or none/uncorrected. | ___ | +| If permutation or Monte Carlo, report the number of permutations/samples; if Monte Carlo, note brain mask and smoothness used, and how smoothness was estimated. | ___ or NA | +| If FWE found by random field theory, list smoothness in mm FWHM and the RESEL count. | ___ or NA | +| If FWE found by simulation (e.g., AFNI AlphaSim), provide details of parameters for simulation. | ___ or NA | +| If not a standard method, specify the method used for finding significance. | ___ or NA | +| False negative discussion: any discussion of failure to reject the null hypothesis (e.g., lack of activation in a particular region) should be accompanied by SNR or effect size of the actually observed effect. | ___ or NA | + + + + +## Follow-up Analyses + + +Enter your response here. + + +## Exploratory Analyses + + +Enter your response here. + + +# Appendices + +## Appendix 1: Examples of fMRI study pre-registrations + +- Pre data collection preregistration following a structure similar to the present template with extensive detail: https://osf.io/2zhve +- Pre data collection preregistration with extensive detail in flow-text: https://osf.io/7q68p/ +- Studies with standard preprocessing approaches (SPM, fMRIprep): https://osf.io/5mx3w; https://osf.io/hndbq [previously collected data] +- Concise preregistration of functional connectivity analyses of existing data: https://osf.io/utqq2 +- Methods analysis on publicly available datasets: https://osf.io/2jxdk/ +- Example of a multi-study pre-registration: https://osf.io/wzd8a