Hi-

Using align_epi_anat.py, I was unable to achieve good alignment, so I did a manual alignment, to make align_epi_anat.py's job easier.

Instead, my brains, which were aligned in original space, became unaligned in Talairach space.

Here is the align_epi_anat.py command I use:

align_epi_anat.py -anat2epi -anat ${subj}_mpra+orig \
-save_skullstrip -suffix _al_junk \
-epi ${subj}_run${run}+orig -epi_base 78 \
-epi_strip 3dAutomask \
-volreg off -tshift off

After Talairaching the anatomy and doing volume registration on the functional data, the volreg, epi2anat and tlrc transformations get catenated, using the following:

cat_matvec -ONELINE \
${subj}_mpra_ns+tlrc::WARP_DATA -I \
${subj}_mpra_al_junk_mat.aff12.1D -I \
mat.r0$run.vr.aff12.1D > mat.r0$run.warp.aff12.1D

Because I already aligned the EPI and anal images by hand, the epi2anat transformation shouldn't be very much.

Yet the Talairached images are poorly aligned.

Please help me if you can.

I can send along script and data sets, as needed.

Thanks,

Jim Waltz