Can't open -source dataset 'copy_af_anat_w_skull+orig'

AFNI Message Board
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Hi, Paul-

Thanks for posting that. Indeed, the overlap does look good, so that is nice. So, if that is not the issue, I wonder if the sform_code and qform_code values of the anatomical are annoying ambiguous. Presuming the dset you put into @SSwarper is a NIFTI dset, what is the output of:

nifti_tool \
    -disp_hdr -field qform_code -field sform_code \
   -infiles   DSET_ANAT

? Or, if it is a BRIK/HEAD file, what is its name?

One other thing I notice from this output is that your anatomical dataset has obliquity in it. The way I can tell is that 2 images are output, and one has "DEOB" in the name---that is what the overlap snapshot program will do if either the overlay or underlay dataset has obliquity (and in this case we know that the Haskins reference template does not have any).

Obliquity is usually something we try to remove from the anatomical before processing (even before @SSwarper, and also before FreeSurfer's recon-all, if you are using that). Even though there isn't a large amount, it is something that different software deal with differently (so, FreeSurfer will apply it while most AFNI alignment programs tend to ignore it), and we want to avoid that mismatch. This post describes 2 ways to remove the obliquity from the anatomical while preserving the coordinate origin (x,y,z)=(0,0,0) and also not smoothing/regridding the data at all.

--pt