Poor alignment, please help


Could you please help to alignment between anatomical image and functional images?
There is significant misalignment between the two.
Here is the script using afni_proc.py…

#!/bin/tcsh -xef
set work_dir = /Volumes/fsmresfiles/MSS/Voss_Lab/DERVISH/Backup
set subj = subj01
afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite
-blocks tshift align tlrc volreg blur mask scale
-copy_anat $work_dir/$subj/epi_$subj.anat+orig
-tlrc_base TT_avg152T1+tlrc
-tcat_remove_first_trs 0
-dsets $work_dir/$subj/epi_$subj.r0*+orig.HEAD
-volreg_align_to third
-volreg_opts_vr -twopass
-align_opts_aea -cost lpc+ZZ -giant_move
-volreg_zpad 4
-blur_size 4.0

I tried several options with different cost function, maybe I might need to try uber_align_test.py
Also, I would like to send the files to check.

Sungshin Kim

I’ve sent a PM to you with instructions on uploading data.

The data was little different than usual - the 4mm3 voxels are a little large, and the obliquity doesn’t bring the dataset very close together, so I suspect that information is wrong in the header. However, I did get something to work reasonably well. Try this command with your data.

align_epi_anat.py -giant_move -anat subj01.anat+orig -epi epi_subj01.r01+orig. -giant_move
-suffix _al2epi -deoblique off -epi_strip None -epi_base 0 -cost lpc+ZZ