Q: I have a question about deformation grids obtained from non-linear registration using nlpfit. These grids contain the 3D displacements at each voxel applied to the source to match the template or to the template to match the source?
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2009-September/002576.html

A: (note that this all presumes you did something like this: where fred.mnc is our input subject)

   bestlinreg fred.mnc template.mnc linear_part.xfm
   nlpfit -init_xfm linear_part.xfm fred.mnc template.mnc

nonlinear_part.xfm

If this is so then the nlxfm is from the source to the target. (after the linear transformation if there is one). This incidentally is why we calculate a model to individual transformation when we want to average a number of transformations during building a model.