Is there a sample script to run end-to-end which provides similar results as the GUI “BrainSuite Anatomical Pipeline” with the same options as you see in the GUI? This will help us to customize it as needed without writing it from the start which may lead to many errors.
Sorry for the slow reply — the scripts that are in the bin folder (brainsuite_anatomical_pipeline.sh and brainsuite_anatomical_pipeline.bat) use the same settings as the GUI and should produce identical results.
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