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Yes, you need to change the number from (1) to (1:1000, or any big number) in the selector. The file will show its frames as separate files that can be selected. Just analyzed some 4D from fsl without any trouble.

Tip: Using (:) does not work. 

2012/11/20 Kathy Pearson <[log in to unmask]>
Using 3D may avoid a problem I have seen when the 4D input is untrimmed.  Trying to apply all the pre-processing steps to only some 3D volumes within the 4D file has given me odd results.  However, if the starting input is trimmed 4D, then the 4D files work as well for me as the 3D.

Kathy Pearson