Hi Lin,
The "expanded functional image" option will cause a three-stage registration to take place (functional -> expanded functional -> structural). This option is useful for partial-FOV data, where one full-FOV volume has been acquired.
The "alternative reference image" option will result in two-stage registration, using the alternative reference in place of the functional data. This option should only be used if the alternative reference is defined in the same space as the functional data.
Paul
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