afni.nimh.nih.gov

Well, I just tried 3dAllineate and 3dQwarp on a couple of 2D images (axial slices from the same subject, about 5 mm apart).

3dAllineate on 2D images no longer works

3dQwarp on 2D images worked just fine

I create 2 single slice datasets (slices 55 and 59) via commands like

3dZcutup -keep 55 55 -prefix a55 anat+tlrc

Then I ran

3dQwarp -base a59+tlrc -source a55+tlrc -maxlev 7 -prefix a55_to_a59

and the results were reasonable.

For histology-to-MRI, you might prefer to add the '-nmi' or '-hel' options to use a different cost function than Pearson correlation.