Hello Rick,
So you're saying that I should change the -tlrc_base in afni_proc.py to match the same template that was used in SSwarper like the following?
afni_proc.py -subj_id SSwarpedSubject \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-copy_anat anatSS.Subj.nii \
-anat_has_skull no \
-dsets *rsfMRI*.nii.gz \
-tcat_remove_first_trs 4 \
-align_opts_aea -ginormous_move -deoblique on -cost lpc+ZZ \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets anatQQ.Subj.nii \
anatQQ.Subj.aff12.1D \
anatQQ.Subj_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
...
And if I understand this correctly, I should be using MNI152_2009c+tlrc (or MNI152_2009_template.nii.gz?) for non-linear alignment and avoid using MNI_avg152T1+tlrc unless its for affine registration?
Thank you.
Edited 1 time(s). Last edit at 08/22/2019 10:13PM by Nshin96.