diff --git a/unit_tests/avwutils/fix_orient/feedsRun b/unit_tests/avwutils/fix_orient/feedsRun
new file mode 100755
index 0000000000000000000000000000000000000000..a56d814bc001d75c5eabcd87764a4dc3281d8e7e
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+++ b/unit_tests/avwutils/fix_orient/feedsRun
@@ -0,0 +1,160 @@
+#!/usr/bin/env python
+"""Test the standard recipe for fixing a broken orientation, from "The labels
+in FSLView are wrong or missing and no conversion to NIfTI can fix this", on
+this page:
+
+https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained
+
+ If this really cannot be fixed at the conversion stage, then it is
+ possible to fix by the follow (only to be attempted after reading the
+ following section on background information on NIfTI orientation):
+ fslorient -deleteorient imagename ; fslswapdim imagename a b c imagename ;
+ fslorient -setqformcode 1 imagename ; where a b c need to be chosen,
+ usually by trial and error, so that the image after this is in the same
+ orientation (as viewed in FSLView) as the MNI152 images. However, unless
+ you have some way of telling left from right in the image (e.g. by a
+ vitamin capsule or clearly known structural asymmetry) this method can
+ easily result in an incorrect left-right labelling and so should not be
+ attempted.
+
+The recipe involves:
+
+ 1. resetting the image affines
+
+ 2. transposing the data array until it is in a
+ RAS orientation
+
+ 3. Enabling the qform affine which, after step
+ 1, should be a diagonal matrix with pixdims
+ as scaling parameters.
+
+Specifically, the recipe is as follows:
+
+ # 1. clear the sform/qform affines
+ fslorient -deleteorient image
+
+ # 2. rotate the data into RAS orientation (exact
+ # command depends on original data orientation)
+ fslswapdim image x z y image
+
+ # 3. reset the qform code. The qform should be
+ # a diagonal matrix, and the image data array
+ # should be in RAS orientation, so after this
+ # step the image should be labelled correctly.
+ fslorient -setqformcode 1 image
+
+
+This recipe makes some key assumptions:
+
+ - fslorient -deleteorient (step 1) deleting/
+ clearing the affines - the qform must be
+ reset to be a scaling matrix.
+
+ - fslswapdim (step 2) not touching the affines
+ when the s/qform codes are 0
+
+These are required so that, in step 3, the qform is a diagonal matrix with
+correct scaling paramaters.
+
+Some bugs were introduced in FSL 6.0.0 (fixed in FSL 6.0.6) which broke the
+above assumptions:
+
+ - fslorient -deleteorient was not clearing the original
+ affines
+ - fslswapdim was applying the rotations/flips to both the
+ data, and to the s/qforms, even if the s/qform codes were
+ set to 0.
+"""
+
+import numpy as np
+import nibabel as nib
+import subprocess as sp
+import shlex
+import sys
+import traceback
+
+def sprun(cmd):
+ sp.run(shlex.split(cmd), check=True)
+
+
+# Test the original recipe for fixing the
+# orientation of an image, as described above
+def test_fix_orient():
+
+ data = np.random.random((10, 10, 10))
+ orig_qform = np.array([[2, 0, 0, 10],
+ [0, 2, 0, -20],
+ [0, 0, 2, 50],
+ [0, 0, 0, 1]])
+ image = nib.Nifti1Image(data, np.eye(4))
+ image.set_sform(np.eye(4), 0)
+ image.set_qform(orig_qform, 1)
+
+ image.to_filename('orig.nii.gz')
+ sprun('imcp orig cleared')
+ sprun('fslorient -deleteorient cleared')
+ sprun('fslswapdim cleared x z y swapped')
+ sprun('imcp swapped fixed')
+ sprun('fslorient -setqformcode 1 fixed')
+
+ fixed = nib.load('fixed.nii.gz')
+
+ new_qform, qcode = fixed.get_qform(coded=True)
+ _, scode = fixed.get_sform(coded=True)
+
+ # new qform should be a scaling matrix (not
+ # necessarily equivalent to the original
+ assert qcode == 1
+ assert scode == 0
+ assert np.all(np.isclose(new_qform, np.diag([2, 2, 2, 1])))
+
+
+# An alternate strategy which involves
+# explicitly clobbering the qform
+def test_fix_orient_alternate():
+ # original qform
+ data = np.random.random((10, 10, 10))
+ orig_qform = np.array([[2, 0, 0, 10],
+ [0, 2, 0, -20],
+ [0, 0, 2, 50],
+ [0, 0, 0, 1]])
+ image = nib.Nifti1Image(data, np.eye(4))
+ image.set_sform(np.eye(4), 0)
+ image.set_qform(orig_qform, 1)
+
+ image.to_filename('orig.nii.gz')
+ sprun('imcp orig cleared')
+ sprun('fslorient -deleteorient cleared')
+ sprun('fslswapdim cleared x z y swapped')
+ sprun('imcp swapped fixed')
+ sprun('fslorient -setqform 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 fixed')
+ sprun('fslorient -setqformcode 1 fixed')
+
+ fixed = nib.load('fixed.nii.gz')
+
+ new_qform, qcode = fixed.get_qform(coded=True)
+ _, scode = fixed.get_sform(coded=True)
+
+ # new qform should be a scaling matrix (not
+ # necessarily equivalent to the original
+ assert qcode == 1
+ assert scode == 0
+ assert np.all(np.isclose(new_qform, np.diag([2, 2, 2, 1])))
+
+
+
+if __name__ == '__main__':
+ tests = [test_fix_orient,
+ test_fix_orient_alternate]
+
+ result = 0
+ for test in tests:
+ try:
+ test()
+ print(f'\nTest {test.__name__} PASSED')
+ except Exception as e:
+ print(f'\nTest {test.__name__} FAILED')
+ traceback.print_exc()
+ result = 1
+
+ sys.exit(result)