Here’s one way, where sFiles is a list of your source files you iterate on with index i:
[sMat, matName] = in_bst(sFiles{i});
ProtocolInfo = bst_get('ProtocolInfo');
sMat.SurfaceFile = 'SubjectName/cortexfile.mat'; % Change this line
outputFile = bst_fullfile(ProtocolInfo.STUDIES, sFiles{i})
bst_save(outputFile, sMat, 'v6');