display p-values overlay

[knutj]

Describe the feature you are missing
A clear and concise description of the feature. Should include information on the expected inputs and output.

FSbrain should be able to load p-value or other MGH with surface data and display it. FDR correction would also be helpfule.

Use Cases

• Your use case for the feature.
• Why do you think that this feature is of general interest, e.g., not only relevant to you.

Automatic p-values maps is very useful when publishing neuroimaging from Fressurfer data.

[dfsp-spirit]

You can already do that, an example that loads an overlay from MGH/MGZ files and displays it with a suitable colorbar in fsbrain can be found in this live notebook, at the very bottom, section Results: vertex-based.

Here is some example code, copied from that notebook:

subjects_dir = file.path(find.freesurferhome()$found_at, 'subjects');
subject_id = 'fsaverage';

lh_demo_cluster_file = system.file("extdata", "lh.clusters_fsaverage.mgz", package = "fsbrain", mustWork = TRUE);
rh_demo_cluster_file = system.file("extdata", "rh.clusters_fsaverage.mgz", package = "fsbrain", mustWork = TRUE);

lh_clust = freesurferformats::read.fs.morph(lh_demo_cluster_file);   # contains a single positive cluster (activation, group difference), the other values are 0
rh_clust = freesurferformats::read.fs.morph(rh_demo_cluster_file);   # contains two negative clusters

vis.symmetric.data.on.subject(subjects_dir, subject_id, lh_clust, rh_clust, bg="curv_light");

If you need correction for multiple comparisons (FDR or something else), stats::p.adjust() should do that for you.

Please let me know whether that helps, or what problems you are facing.