Dear Aaron,
by default, SPM uses a lot of auto-configuration magic (toolboxes, spm_orthviews plugins, batch system, embedded fieldtrip...) that does not work out of the box in a compiled context. Therefore, SPM has its own compile script spm_make_standalone.m, which lives in the config/ folder of your SPM installation. Most likely, you will need to integrate this script in the build process of your standalone application.
Volkmar
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