sourcespace = ft_read_headshape('Subject01-oct-6-src.fif', 'format', 'mne_source'); %load the fif file from /bem directory 
sourcespace = ft_convert_units(sourcespace, 'mm');
figure
ft_plot_mesh(sourcespace)

cifti = ft_read_cifti('path_to_atlas');

indxV1 = []; %variable to hold vertex number(s) of interest
x = 1;
y = 0;
for k = 1:length(cifti.v1_msmall) % cifti.v1_msmall is an area within an atlas registered on the conte69 brain
    if sourcespace.orig.inuse(k) == 1
        y = y+1;
        if cifti.v1_msmall(k) == 1
            indxV1(x) = y;
            x = x+1;
        end
    end 
end

indxV1pnt = zeros(length(indxV1),3); %variable to hold grid points of interest
for j = 1:length(indxV1)
    indxV1pnt(j,:) = sourcespace.pnt(indxV1(j),:);
end
% can now use cfg.grid.pos = indxV1pnt when calling ft_prepare_leadfield