There's really not a perfect solution. We know that aligning pediatric data to adult templates is not ideal. The basics are:

1. At age 6, cerebral volume is about 95% of that of an adult (Lenroot & Giedd, 2006).
2. However, grey matter follows an inverted U-shape, which peaks at different times for different cortical (and subcortical) regions (Lenroot & Giedd, 2006).
3. In general, using a nonlinear warp can help with local deformations (Kochunov et al., 2002)
4. Some estimates show that 8 year olds have 20% more deformation when going to an adult template vs. a child template (Yoon et al., 2009)

Using covariates is still a voxel-wise process in 3dttest++, so it's not going to fix the problems with deformation distances and transform accuracies. I would be hesitant of how much to trust the alignment of small cortical and subcortical areas. You might consider the following:

1. Wilke et al. (2008) have a Template-o-Matic that has the ability to generate a template from 4-19 years or so.
2. Aligning the pediatric data to our Haskins Pediatric Template (nonlinear preferred), Aligning the adult data to TT_N27. Trying to make indirect comparisons between the samples.
3. Create your own template based on the sample
4. Make extended use of the phrase "exploratory" in your limitations section and do any of these three or your current path of using the TT_N27.