Extracting and visualizing `verywise` results

Serena Defina

2026-01-08

verywise output

Check out the output directory. You should see something like this [TODO: add image]

Extracting mean/median cluster values

Sometimes, you may want to extract the mean or the median value of a specific cluster from your results, for example to use this in further analysis. You can do this in verywise using the significant_cluster_stats() function.

Note: ideally, you should run your analyses with save_ss = TRUE or save_ss = "path/to/ss", or you have called build_supersubject() in your pipeline, for this to sun smoothly.

# Extract mean from significant clusters
df <- significant_cluster_stats(stat = "mean", # or "median"
                                ss_dir = "path/to/ss_directory", 
                                res_dir = "path/to/results", 
                                term = "age", # term of interest 
                                measure = "thickness", 
                                hemi = "lh")

Visualizing results

To inspect and plot your results, you can use our interactive web application, verywiseWIZard. You can run this locally or try it out here.

Note: if you are using the online version of the WIZard, with results hosten on GitHub, you may want to look into the move_result_files() helper function, to organise your results in a way that is safe (i.e., does not expose individual level data) and quick.

Plots can also be generated using verywise like so:

# Plot result brain map (requires FreeSurfer for templates and reticulate for interface with Python-based plotting libraries)
plot_vw_map(
  term = "age",
  hemi = "lh",
  measure = "area",
  res_dir = "/path/to/output",
  outline_rois = c("entorhinal", "precuneus"),
  fs_home = "/path/to/FREESURFER_HOME"
)