I am trying to create a tool that has EPI outlines like the nibabel example (https://nipy.org/nibabel/coordinate_systems.html#the-affine-as-a-series-of-transformations), but with the ability to move the outlines by hand. The best tool I know for manual movements of scans is ITK-SNAP, so I have been trying to import "outline" EPI scans from nibabel. This is not working properly (EPI images appear much larger than anatomical images when overlaid), and I am not sure why.

Here is some code that I have used to create the EPIs:

# create outline data
data = np.ones((192, 192, 27))
data[1:-1, 1:-1, 1:-1] = 0   # creates an outline only

# create blank rotation with scaling
rot = np.diag([0.8, 0.8, 0.8, 1])

# create a nifti image and save
img = nb.Nifti1Image(data, rot)
img.set_qform(img.affine, 1)
img.to_filename('epi.nii.gz')

I added the line setting the qform based on this comment: #801 (comment)

ITK-SNAP still cannot properly read the orientation of the outline scan. However, FSL is able to read it just fine. Are there other nibabel methods required to properly prepare a header for use in ITK?