Thanks for the clarification. Once you have computed the source using a volume source space. It is possible to import the .nii
masks as Scouts, and these scouts will indicate which indices to mask on the source reconstruction.
MRI and a mask (left motor cortex)
Scout created with mask.nii
file, and its (236) indices, which indicate the source vertices in the Scout.
This is when the source space is defined, so the number of vertices.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource