You may want to use a resampled or higher resolution template like the MNI152_1mm_uni+tlrc or the newly introduced (in the latest binary distributions) MNI152_T1_2009c+tlrc. Both are at 1mm resolution. The latter is a nonlinearly generated template that I think will be more useful. MNI has 0.5 mm3 resolution templates available too that are downloadable at :
http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009.
The nonlinear, asymmetric version that is distributed with AFNI has been tweaked a bit to fit into byte-size (0-255) values.
Do you need a single voxel location or a region? If you really only want specific coordinates, then you could warp the xyz coordinates with Vecwarp using the transformation computed by @auto_tlrc. If the coordinates are stored as tags in a dataset by the Tagset plugin, you can have the plugin write the tag coordinates to a file and use Vecwarp to move those coordinates. Then you might use 3dUndump to create a new dataset or the Tagset plugin to use the new tag locations in an existing dataset.