qform/sform differ

[jcohenadad]

julien-macbook:~/code/sct/data/exvivo_template/template $ fslhd template.nii.gz 
[...]
qform_name	Unknown
qform_code	0
qto_xyz:1	0.080000 0.000000 0.000000 0.000000 
qto_xyz:2	0.000000 0.080000 0.000000 0.000000 
qto_xyz:3	0.000000 0.000000 0.080000 33.680000 
qto_xyz:4	0.000000 0.000000 0.000000 1.000000 
qform_xorient	Left-to-Right
qform_yorient	Posterior-to-Anterior
qform_zorient	Inferior-to-Superior
sform_name	Unknown
sform_code	1
sto_xyz:1	-0.080000 0.000000 0.000000 0.000000 
sto_xyz:2	-0.000000 0.080000 0.000000 0.000000 
sto_xyz:3	-0.000000 0.000000 0.080000 33.680000 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 
sform_xorient	Right-to-Left
sform_yorient	Posterior-to-Anterior
sform_zorient	Inferior-to-Superior

Causing the following crash:

Straighten the spinal cord using centerline/segmentation...
Creating temporary folder (/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114030.722928-straighten_spinalcord-cykcwclc)
Copy files to tmp folder...
Image /private/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114011.750277-register_to_template-rthcfks3/template_seg.nii.gz has different qform and sform matrices. This can produce incorrect results. Consider setting the two matrices to be equal by running:
sct_image -i /private/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114011.750277-register_to_template-rthcfks3/template_seg.nii.gz -set-sform-to-qform -o /private/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114011_same-affine.750277-register_to_template-rthcfks3/template_seg.nii.gz.
Traceback (most recent call last):
  File "/Users/julien/code/sct/spinalcordtoolbox/scripts/sct_register_to_template.py", line 1281, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/sct/spinalcordtoolbox/scripts/sct_register_to_template.py", line 533, in main
    sc_straight.straighten()
  File "/Users/julien/code/sct/spinalcordtoolbox/straightening.py", line 111, in straighten
    Image(self.centerline_reference_filename, check_sform=True).save(os.path.join(path_tmp, "centerline_ref.nii.gz"))
  File "/Users/julien/code/sct/spinalcordtoolbox/image.py", line 311, in __init__
    raise ValueError("Image sform does not match qform")
ValueError: Image sform does not match qform

Suggested fix: match qform/sform and update this template.

Related to spinalcordtoolbox/spinalcordtoolbox#3174

[jcohenadad]

@joshuacwnewton I'm a bit lost with this issue-- didn't we force the copy of the sform/qform to avoid this crash? Or if not, shouldn't we output a more helpful message, such as: "To fix the problem, run sct_image -i PAST-IMAGE-NAME -set-sform-to-qform"?

[jcohenadad]

To temporarily overcome the issue i did this:

sct_image -i template.nii.gz -set-sform-to-qform
sct_image -i mask_spinalcord.nii.gz -set-sform-to-qform

[joshuacwnewton]

@joshuacwnewton I'm a bit lost with this issue-- didn't we force the copy of the sform/qform to avoid this crash? Or if not, shouldn't we output a more helpful message, such as: "To fix the problem, run sct_image -i PAST-IMAGE-NAME -set-sform-to-qform"?

We do output a message, but it was written using a separate logger.error statement, so it should show up above the actual error message.

https://github.com/neuropoly/spinalcordtoolbox/blob/60ea08c9d664cf403f2982f8f5c8ae1cc5d704a3/spinalcordtoolbox/image.py#L307-L311

I agree that the log isn't clear enough the way it is now.

[jcohenadad]

Ah! Yes you are right. It even appears in red (which is good):

[joshuacwnewton]

Ahh, that's a useful screenshot! Because we use the absolute paths, the message is very verbose, like a wall of text. It is easy to gloss over and ignore, I think. So, some work could be done to make it more readable.

[jcohenadad]

suggestion:

⚠️ The following image has different qform and sform matrices: /private/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114011.750277-register_to_template-rthcfks3/template_seg.nii.gz .

This can produce incorrect results. Consider setting the two matrices to be equal by running:
sct_image -i /private/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114011.750277-register_to_template-rthcfks3/template_seg.nii.gz -set-sform-to-qform -o /private/var/folders/s8/4qnm5q1n261ch35b5kkclsb00000gn/T/sct-20210316114011_same-affine.750277-register_to_template-rthcfks3/template_seg.nii.gz.

Traceback (most recent call last):
  File "/Users/julien/code/sct/spinalcordtoolbox/scripts/sct_register_to_template.py", line 1281, in <module>
    main(sys.argv[1:])
  File "/Users/julien/code/sct/spinalcordtoolbox/scripts/sct_register_to_template.py", line 533, in main
    sc_straight.straighten()
  File "/Users/julien/code/sct/spinalcordtoolbox/straightening.py", line 111, in straighten
    Image(self.centerline_reference_filename, check_sform=True).save(os.path.join(path_tmp, "centerline_ref.nii.gz"))
  File "/Users/julien/code/sct/spinalcordtoolbox/image.py", line 311, in __init__
    raise ValueError("Image sform does not match qform")
ValueError: Image sform does not match qform