3dAllineate is deliberately not designed for registering a 2D slice into a 3D volume, as that is a tricky thing to do well even with good data.

Registering an actual activation map into a volume is not even a good idea. You could try to register a 2D echo-planar image into a 2D T1-weighted slice, but that isn't what your post asks for.

If you wish to create a single-slice dataset cut out of a 3D volume, the simplest way is with 3dZcutup. However, your dataset is coronal, so the Z cutting will be along the A-P axis. To get an axial slice, you'll have to resample your dataset to be axial. For example:

3daxialize -prefix TempAx -axial Coronal+orig
3dZcutup -keep 57 57 -prefix Ax57 TempAx+orig
rm TempAx+orig.*

The slice index '57' above you will have to figure out by viewing in the AFNI controller, with Voxel Indexes turned on in the upper-left coordinate display (right click in the coordinate display box, choose the 'Voxel Indexes' item). The 'voxel z' index is the slice index in the dataset as stored on disk.

I'm giving you these detailed instructions in case they help you, but my feeling is that you don't really know quite what you want to do. I re-iterated that trying to register an actual activation map to an anatomical image will not work. You can try to register an antomical slice to an EPI slice, but that will only work if you are very careful in choosing the anatomical slice. Note that I say register the anatomical slice to the EPI slice -- then the activation map derived from the single-slice EPI time series dataset should properly overlay the anatomical slice.