Thank you Rick. I ran @SSwarper and the jpeg files look reasonable. When I tried to feed the inputs back into my afni_proc.py script however, it resulted in an error message indicating that the +tlrc warp dataset was missing. It seems afni_proc.py was trying to find the file "anatQQ.MNI152_2009_template_SSW.nii.gz+tlrc" which I don't have.
Would it be safe to replace the endings ( "+tlrc" with ".nii") as the anatQQ.MNI152_2009_template_SSW.nii.gz.nii is the skull stripped and warped file?
afni_proc.py script I altered:
-tcat_remove_first_trs 0 -tlrc_base MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets anatQQ.MNI152_2009_template_SSW.nii.gz.nii anatQQ.MNI152_2009_template_SSW.nii.gz.aff12.1D anatQQ.MNI152_2009_template_SSW.nii.gz_WARP.nii \
-volreg_align_to last -volreg_align_e2a -volreg_tlrc_warp -blur_size \
4.0 -regress_stim_times \
Thank you!
Tamara
