Hello,
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_align_e2a \
-volreg_tlrc_warp \
-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.
Sincerely,
Sungshin Kim
