Absolutely. I uploaded the script I ran as a .txt in my files -- Create_Run_Preprocess_Script_11b_SSwarp -- (I assume/hope you have access to that?). The script is roughly running example 11b from afni_proc.py to process my resting state data with my anatomical but I have it running @SSwarper first to skull strip and put in MNI space and then using those warp files for the afni_proc.py.
The relevant lines for the @SSwarper would be:
@SSwarper -input ${sid}_${series}_anat+orig \
-subid ${sid}_${series} \
-odir ${sid}_${series}_anat_warped \
-base ${template}
The given variables are set in the following ways earlier in the script:
set template = "/home/keith/abin/MNI152_2009_template_SSW.nii.gz"
foreach id(004) # a foreach loop to go through each subject
# 001 002 003 004... etc.
set sid = "Sub_${id}"
set series = "01" # there was only ever 1 scan per subject
#### Everything else including the @SSwarper commands and then afni_proc.py ######
end
Thanks!
Edited 1 time(s). Last edit at 06/29/2020 08:04PM by kxd344.
