...and of course I figure it out shortly after posting: it needed -base first.
@SSwarper -base MNI152_2009_template_SSW.nii.gz -input $anatFile -subid sub-${subject}_ses-${session} -odir ${outDir}"
...and of course I figure it out shortly after posting: it needed -base first.
@SSwarper -base MNI152_2009_template_SSW.nii.gz -input $anatFile -subid sub-${subject}_ses-${session} -odir ${outDir}"
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