afni.nimh.nih.gov

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.