Thanks Alfonso, so when I am batch scripting for an ROI-ROI analysis in native space is the following correct;

BATCH.Setup.nsubjects=n;
for i= 1:161
f=spm_select('FPList',dir, '^u.*\.img$');
BATCH.Setup.functionals{n}{1}{i}=f(i,:);
end
BATCH.Setup.structurals{n}=fullfile(root,sub_ind{n},'T1_Data','seg4coreg.nii');
%BATCH.Setup.roiextract=1;
BATCH.Setup.roiextract=3;
batch.Setup.roiextract_rule = {1, '^sw', ''};

Best wishes,

Peter