Hi Lewis,
I assume you are using spm_jobman('run', ...) to populate and run your job. This call has two optional output arguments, the collected outputs from each batch module and the job actually run. So, [~, matlabbatch] = spm_jobman('run', ...) will give you the job populated with the actually used data. Note that these data will replace the dependencies from your template. You can then save this matlabbatch variable to a .mat file or use gencode(matlabbatch) to produce MATLAB code for the job variable.
Hope this helps,
Volkmar
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