Hi All,

I think the de-oblique option did the trick in conjunction with the other suggestions. Here's what I did. The only issue now is that I think I need to add the -dxyz dd option to change the file to a lower resolution image as the file size is huge right now. Thanks for your help.


3dWarp -deoblique t1h.nii
3dcalc -prefix t1hd -a warped+orig -expr 'a'
rm warped+orig*

3dUnifize -prefix t1hd_U -input t1hd+orig
3dSkullStrip -input t1hd_U+orig -prefix t1hd_US -niter 400 -ld 40
3dAllineate -prefix t1hd_USA -base /opt/afni/TT_N27+tlrc \
-source t1hd_US+orig -twopass -cost lpa \
-1Dmatrix_save t1hd_USA.aff12.1D \
-autoweight -fineblur 3 -cmass

3dQwarp -prefix t1hdQw -duplo -useweight -blur 0 3 -base /opt/afni/TT_N27+tlrc -source t1hd_USA+tlrc

align_epi_anat.py -anat t1hd_U+orig -epi ${id}_zpad.nii \
-epi_base 3 -epi2anat -ginormous_move

3dNwarpApply -prefix ${id}_zpad_d_QW -source ${id}_zpad.nii \
-nwarp 't1hdQw_WARP+tlrc t1hd_USA.aff12.1D "${id}"_zpad_al_reg_mat.aff12.1D' \
-master t1hdQw_WARP+tlrc