Is the mask created from SaveMsk in the AFNI GUI a binary mask? If not, how do I change the mask to a binary mask?
It should be saved as what I refer to as an “ROI map”. 3dClusterize (the command line form of clusterizing) or the clusterizer in the GUI work the same way: they threshold and get rid of tiny islands, and leave you with a map of remaining clusters. These are “labeled” by painting each voxel in a cluster with a given integer value: by default, the largest cluster is all 1s, the next largest is all 2s, etc. It is nice to have the identity of each cluster preserved for later processing-- such as calculating average time series with an ROI, or using 3dNetCorr to calculate a correlation matrix across ROIs, etc.
If you want to binarize the output mask/map, then you can use 3dcalc:
3dcalc -a DSET -expr "bool(a)" -prefix DSET_AS_BINARIZED_MASK