Hi-

I don't see why the 3dcopy would change this parameter. I assume it has to be the qform_code and sform_code values from FMRIprep output that are defining the space. What is the output of the following from your FMRIprep output:

A:

nifti_tool -disp_hdr -field qform_code -field sform_code -infiles DSET_EPI

B:

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

You can change the header property of space with 3drefit, but before discussing that, I would like to understand what is happening (and likely what *should* be happening). I am not very familiar with FMRIprep, so please let me know what A and B outputs are.

And for the "should be happening" part, am I correct that your FMRIprep command above should be outputting the EPIs in alignment with the subject anatomical (so, basically in a "native" subject space)?

--pt