That depends on what you want to do with them. If you just want to look at them, then AFNI can do that without any previous extraction. If you want to put them into ANALYZE-7.5 formatted files for SPM to use, then you can use a command like
3dAFNItoANALYZE -4D aname 'dset+orig[32]'
which will write files aname.hdr and aname.img from sub-brick #32 of dataset "dset+orig". To decide that you want sub-brick #32, you'd probably want to look at the output of "3dinfo dset+orig". When you run 3dDeconvolve, it helps mightily if you use the -stim_label and -glt_label options to put the proper labels on the resulting sub-bricks. This makes it much easier to tell which sub-brick is what, both in the AFNI menus and in 3dinfo.

Most command line (3dSomething) programs in AFNI can process sub-bricks directly, without prior extraction. The syntax is the same as used in the example above, with the sub-brick index given in square brackets. For the melancholy details of command line dataset names, see the output of "afni -help", under the "INPUT DATASET NAMES" header.

bob cox