rick reynolds Wrote:

> If you want the EPI aligned to the
> anat, consider
> adding -epi2anat, and maybe something like
> -master_epi 3.5
> (note that 3.5 mm is the voxel size that
> afni_proc.py would
> use if you were asking it to write the analysis
> script).

Hi Rick and everybody,

I was wondering where this 3.5 mm comes from (should it be 0.94 since we are trying to align the epi to the anatomic)? Anyway, I still have spent some time poring over align_epi_anat.py and tried several things but i am not getting what I would like. Specifically, the resulting grids are still different for each of them. Perhaps what I am looking for does not make sense using AFNI: but I thought that it would be helpful to explain this again.

So, I have an anatomic dataset of dimension 110 x 208 x 202 voxels of size 1.5x0.94X0.94 mm^3 and a functional time course sequence of dimension 64x64x30x105 (105 timepoints). So what I am looking for is a registration of the functional data for motion and other correction and also to match the grid of the functional with the anatomic. I would end with a grid in 3-d where the functional can be overlaid on the anatomic (and thus the grid matches for one matches the other). How can this done?

Many thanks again!

Best wishes,
Ranjan