Overlaying plots and transparent thresholding | Transparent thresholding | Running a vertex-wise linear model | Plotting significant and subthreshold outcome | Overlaying plots together | Overlaying HippUnfold hippocampal plots | Overlaying SubCortexMesh subcortical plots | References:

Example analyses with VertexWiseR - Example 3 | Requirements | Extracting ASeg subcortical surfaces | Example analysis on the thalamus and caudate nuclei | Analysing all subcortices together | References:

1. How to make VWRfirstrun() ignore the system’s Python environment when starting a fresh installation | 2. How to make VWRfirstrun() use a specific Python installation | 3. VWRfirstrun() shows the message “Clearing reticulate’s uv cache…” | 4. About the message: “Would you like to create a default Python environment for the reticulate package? (Yes/no/cancel)” (reticulate < 1.41.0) | References:

Example analyses with VertexWiseR - Example 1 | Installing VertexWiseR and checking for requirements | Example analysis 1: linear model of age and cortical thickness, and meta-analytic decoding | References:

Example analyses with VertexWiseR - Example 2 | Example 2: Mixed effect model of intervention-related changes on hippocampal thickness | Example 2 follow-up: plotting and post-hoc analyses of hippocampal clusters across regression models | References:

Summary | Extracting cortical surface data: from FreeSurfer | Extracting cortical surface data: from HCP processing, sMRIprep, fMRIprep, ASLprep or XCP-D | Extracting cortical surface data: from CAT12 | Extracting hippocampal surface data: from HippUnfold | Extracting subcortical surface data: from SubCortexMesh | References: