Hi, Korann/Vittal-
This syntax doesn't look quite right; I think it is missing a "-input ..." option name. I think this is what you would want (and just spaced one per line, for readability):
@SSwarper \
-input CSRI-004-1-Structural.nii \
-base MNI152_2009_template_SSW.nii.gz \
-subid CSRI004 \
Note that in this modern form, then your output files won't have the "-base" in it. I see now why the "-base" appears in the name-- as Rick rightly pointed out, your AFNI version was quite old, and the syntax of @SSwarper had been updated since then (going from just listing a few files to have option flag names, for greater generalized usage). So, instead of:
-copy_anat anatSS.-base.nii \
...
-tlrc_NL_warped_dsets \
anatQQ.-base.nii \
anatQQ.-base.aff12.1D \
anatQQ.-base_WARP.nii \
it would probably be more like:
-copy_anat anatSS.CSRI004.nii \
...
-tlrc_NL_warped_dsets \
anatQQ.CSRI004.nii \
anatQQ.CSRI004.aff12.1D \
anatQQ.CSRI004_WARP.nii \
(or, you could use a variable name instead of "CSRI004", for generalized application).
Also, in your @SSwarper command call, this file is your input:
CSRI-004-1-Structural.nii
but in your afni_proc.py command, this file is a follower:
-anat_follower anat_w_skull anat CSRI004_SurfVol.nii \
. I would have thought those should be the same files?
--pt
