Here's my problem:

I have two days of anatomical/epi datasets for each subject I want to analyze.

I have defined ROI masks on day 1 anatomicals and would like to align the statistical maps (from both days) into this space. Ultimately, everything will have to be in the same space because I'll be doing analyses involving the union and intersection of statistically relevant voxels between both days worth of data for specified ROIs.

The other complication is that the functional and anatomical datasets on a given day also may be out of alignment.

Current approach:
*align day 1 structural to day 1 functional with 3dAnatnudge
*align day 2 structural to day 2 functional with 3dAnatnudge
*determine movement parameters between nudged anatomicals (from both days) and day1 structural using 3dvolreg
*use 3drotate (with rotation/translation parameters from shifted datasets generated in previous step) to apply to day 1 and day 2 functional datasets

Two questions:
Is this needlessly complex--or is there a recommended better way?
If I use the 3drotate method using output of 3dvolreg, does my selection of gridparent dataset matter greatly?

Thanks,
Jane Lange