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