Dear Priyangi,
Go with a "Coregister: Reslice step", for "Image Defining Space" choose one of your preprocessed, normalized files, for "Images to Reslice" select the atlas file. For "Interpolation" you have to go with "Nearest neighbour", as you want to preserve different regions to be coded by different values. Make sure that the atlas file is in the same space as your preprocessed data (usually MNI space). In some toolboxes like the Anatomy toolbox (which might by the way be interesting, as it offers cytoarchitectonic labels based on several subjects and not just a single one, and it also provides probabilistic versions) the origin is different, in that case you first have to adjust the file to reflect e.g. MNI space.
Best
Helmut
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