Andy-
Perhaps you can tell me if your overlay is a voxelwise dataset
(e.g. you are painting the surface with a NIfTI *.nii file) or has
been converted to a mesh iso-surface (e.g. a OBJ, GII, MZ3, etc
mesh).
If you are loading a NIfTI voxelwise dataset, you adjust the
threshold using the two min and max values in the Overlay panel.
This is described here
https://www.nitrc.org/tracker/index.php?func=detail&aid=8092&group_id=984&atid=3730
for example, in the following image the threshold for the reddish
overlay has been set to 2..12, setting the range to 1..12 will lead
to a larger region seurviving the threshold and a range of 6..12
would lead to a more focal region. Choose you threshold based on
your correction for multiple comparisons.
https://www.nitrc.org/tracker/download.php/984/3730/8092/791/fmri_paint_surface.jpg
On the other hand, when you use the
"Advanced/ConvertVoxelwiseVolumeToMesh" you will be asked to select
a NIfTI image and a threshold. The size of the resulting blob
depends on your threshold. Setting a Value of 1 would result in a
larger blog than a stringent threshold like 12. In this latter
case, you can use the preferences feature you mentioned to decide
what happens at the edge of the brain: since we typically only
compute statistics inside the brain there is often a sharp cutoff
at the edge of the cortex. This is described here:
https://www.nitrc.org/plugins/mwiki/inde...