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To start this process, in the Extraction preferences, select Object Finding: Interactive/User Defined and Extraction Method: Optimal.  Then, as in the boxcar case FIREHOSE will solve for the wavelength map and present you with a first-pass sky subtracted frame as shown here: Image Removed 

In this case I have zoomed in to the line of interest, an H alpha profile of a z = 1.7 galaxy.  Now, rather than defining the center of the aperture in spatial coordinates, you must define the bounds of the wavelength region of interest where you want to fit the profile.  Since wavelengths run vertically in FIREHOSE frames, this means you need to set the bottom and top of the bounding region.