Hi, Clément-

You can change the header information for the dset in question, to correc the space from being "ORIG" to being "NMT", with:

3drefit -space NMT warp2std_nsu.nii.gz

That should adjust all related properties of the dset (qform and sform, for example)

nifti_tool -disp_hdr -infiles EEE.nii | grep qform

... and the last column that is output should be a '5' (which means the template is technically classified as 'NIFTI_XFORM_TEMPLATE_OTHER'; you can read more about the fascinating discussion of this variable and recent expansions to its set of values here:
[www.nitrc.org])

I believe the expectation is that every reference base will be something that has non-ORIG space value; afni_proc.py has to do work to predict the output names, and this seems a safe assumption. A reference "space" name can be assigned as above; however, probably some caution+circumspection should be used in applying this haphazardly (for interpretation's sake). In this present case, having an NMT template version with "ORIG" space is a mistake/relic of another era, and so using 3drefit to fix the header makes sense. For future work, using the 'modern' NMT_SS.nii.gz file that *does* have a space name will be highly preferable for pipeline flows.

We have been doing a lot of work with non-human templates (and "we" means Daniel Glen, basically), and non-human templates should still have non-ORIG space values. Actually, it is basically *because* of such a proliferation of non-MNI and non-Talairach templates that the new [qs]form value of '5' was created. If a given template of interest doesn't have a space name, please let us know; we would like to start helping people standardize/utilize these kinds of space names.

--pt