Hi Patrick,
Your EPI dataset is screwed up. It is completely out of alignment with the Anat but that's OK because you can go straight to TLRC space. The big problem is that you have your voxel dimensions wrong. 3dinfo shows me that you have voxel dimensions of 0.938x0.938x0.938 mm. I suspect the error came about in the to3d step. This needs to be fixed. To illustrate the solution however, I pretended that the dimentions were 3.5x3.5x3.5 (just a guess to show you how the alignment to TLRC can be done).

3drefit -xdel 3.5 -ydel 3.5 -zdel 3.5 -keepcen run1_EP+orig. (You should specify all your EPI datasets on this command line)
@Align_Centers -base gz15_MP+orig. -dset run1_EP+orig. (Similarly here, all EPIs on this command line)

(Now do your motion correction on all you EPI data)

@auto_tlrc -suffix NONE -input gz15_MP+orig. -base TT_avg152T1+tlrc -ok_notice (If your @auto_tlrc does not force you to use the -ok_notice with this template then you MUST get the latest version of AFNI)
@auto_tlrc -suffix NONE -input run1_EP_shft+orig.'[0]' -base TT_EPI+tlrc (This is transforming the EPI to tlrc space. This has to be done on one of the sub-bricks only. I selected '[0]' from run1, assuming that is the one you use as a base for the motion correction of all runs.)

To recover a high resolution of the anatomical dataset use (the -dxyz option in @auto_tlrc usage mode 1 does not do anything):
adwarp -apar gz15_MP+tlrc. -dpar gz15_MP+orig. -dxyz 1.0 -force

To put the EPI time series in TLRC use:
adwarp -apar run1_EP_shft_0+tlrc. -dpar run1_EP_shft+orig. -dxyz 3.5

Now you should have gz15_MP+tlrc and run1_EP_shft+orig in good alignment (I have verified that with the data you sent me)

You can repeat the last adwarp command on the remaining EPI runs. For example:
adwarp -apar run1_EP_shft_0+tlrc. -dpar run2_EP_shft+orig. -dxyz 3.5
Note that the -apar is the same, that's because you should have done motion correction in orig space before)

(This message will also be posted on the message board)
cheers,
-ziad