Hello! I am looking for assistance with utilizing 3dvolreg for motion correction. After running our 3dvolreg motion correction, we register our EPI to our anatomical utilizing FLIRT within FSL. When we are comparing our motion corrected functional file with the original functional file, we don't notice any differences, which leads us to think there is no motion correct occurring. We have reviewed our step in utilizing FSL's FLIRT, and they are correct, so we believe the issue may be that we are either missing an option or have incorrectly used one in 3dvolreg. Is there anything in our script that we can change to fix this? Thank you!
See script below:
# echo
# echo "Processing functional for ${subj}... "
# echo
# echo "Motion correction..."
# cd ${subjectsDirectory}/rest
# mkdir motion
# 3dvolreg -zpad 4 -tshift ii -base 0 \
# -1Dmatrix_save motion/${subj}_vr -nomaxdisp -1Dfile motion/${subj}_vr_motion.1D \
# -prefix ${subj}_resting_moco.nii.gz rest.nii.gz
