Daniel,

Here is the command we used:

align_epi_anat.py -anat s003_anat+orig -epi s003_facename_r02+orig \
-suffix _al -epi_base 179 -save_vr -child_epi s003_facename_r??+orig.HEAD


On further exploration, it seems that the issue is related to where to3d places the oblique epis in space when it makes the BRIK from the Dicom files....the resulting BRIKs have these weird dimensions (placing them down in the right corner) even before entering into the alignment program:

R-to-L extent: -126.000 [R] -to- 126.000 [L] -step- 4.000 mm [ 64 voxels]
A-to-P extent: 8.215 [P] -to- 124.215 [P] -step- 4.000 mm [ 30 voxels]
I-to-S extent: -221.591 -to- 30.409 [S] -step- 4.000 mm [ 64 voxels]

Any suggestions?

Lisa