afni.nimh.nih.gov

Hi-

Thanks; I see you are warping to MNI space, so an example @SSwarper command with some of your variable name(s) would be:

set subj = sub-000   # or, whatever your subject ID would be
set template = MNI152_2009_template_SSW.nii.gz 

@SSwarper             \
        -input  ${anat_dir}/mprage+orig           \
        -base   ${template}           \
        -subid  ${subj}           \
       -odir   ${anat_dir}/SSW          \

and then, as noted in the @SSwarper help file:

afni_proc.py                                                  \
      [...other stuff here: processing blocks, options...]        \
      -copy_anat ${anat_dir}/SSW/anatSS.${subj}.nii                               \
      -anat_has_skull no                                          \
      -volreg_align_to MIN_OUTLIER                                \
      -volreg_align_e2a                                           \
      -volreg_tlrc_warp \
      -tlrc_base ${template}              \
      -tlrc_NL_warp                                               \
      -tlrc_NL_warped_dsets                                       \
         ${anat_dir}/SSW/anatQQ.${subj}.nii                                       \
         ${anat_dir}/SSW/anatQQ.${subj}.aff12.1D                                  \
         ${anat_dir}/SSW/anatQQ.${subj}_WARP.nii