bob cox wrote:

> I might do (3) first, then (0), if there is likely to be much
> movement between runs. That is, average the 3dvolreg-ed EPI
> volumes and register THAT to the T1 volume.

So this is what i intent doing:

0. timeshirt
1. concatenate
2. motion correction the concatenated runs (3dvolreg (no use of 1Dmatrix_save))
3. edge detect
4. deconvolve
5. nonlinear fit
6. compute percent AUC.
7. align and normalise
7a. average motion corrected volumes (3dTstat -mean)
7b. register avg from 7a to T1 anatomical
7c. use matrix from 7b to align %AUC files to the T1 anatomicals
7d. auto-Talairach the T1 anatomicals
7e. adwarp -apar skullStrippedAnatomy_at+tlrc.HEAD -dpar alignedAucFrom7c+orig.HEAD

Can you see any problems with this alignment process? Particularly since I leave out the concatenation of the transformation matrices. I'd like to avoid registering all the volumes in my original EPI time series to the anatomicals.

Thanks,

Colm.