Hello.

The issue with 'Non-orthogonal rotation or shearing found inside the affine matrix in this NIfTI file' pops up because the nifti file, when created, had some errors/corruptions in the header information.
I have faced such issues with the imaging data I work with, and more often than not, using load_untouch_nii (instead of load_nii) would solve the issue! (a.k.a the solution 2 above). Hence, look through the w2mhs code and use load_untouch_nii wherever necessary.
You can also check for more solutions on SPM archives (https://www.jiscmail.ac.uk/cgi-bin/webad...).