I am having troubble aligning a few of my images. Specifically, I have tried aligning the epi to the anatomical image as well as aligning the anatomical to the epi. The actual epi image is proportional to the tlrc image; however, for some reason the image is pushed forward towards the frontal lobe and falls short toward the occipital lobe. Are there any afni codes that can solve this problem?


here is the scrip I have been using:

#!/bin/tcsh
#
foreach subj ( 23C )
cd /Volumes/Yay_HD/VS_motion_kj/subjects/$subj

rm -vi *_align-py_stdout.txt
# Aligns anatomy volume to EPI volumes
align_epi_anat.py \
-anat ${subj}_Struct_brain+orig \
-epi ${subj}_Run3_nd+orig \
-epi_base 62 \
-suffix _e2a \
-child_epi ${subj}_Run1_nd+orig ${subj}_Run2_nd+orig ${subj}_Run4_nd+orig \
-anat_has_skull no \
-partial_axial \
-epi_strip 3dAutomask \
-tshift off \
-volreg_method 3dvolreg \
-volreg on \
-volreg_opts -twopass -heptic -zpad 4 \
-maxdisp -verbose -AddEdge | & tee ${subj}_align-py_stdout.txt
# Don't forget to view AddEdge directories! :)
end
echo 'done.'; date