ivadomed / ivadomed/data-testing
qform=2 on testing data
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Description
On the **data_testing/sub-unf01/anat/sub-unf01_T1w.nii.gz** data, fslhd gives:
~~~
qform_code 0
qto_xyz:1 1.000000 0.000000 0.000069 -64.129700
qto_xyz:2 -0.000011 0.986856 0.161602 -59.711037
qto_xyz:3 -0.000068 -0.161602 0.986856 -2.379487
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 2
sto_xyz:1 1.000000 0.000000 0.000069 -64.129700
sto_xyz:2 -0.000011 0.986856 0.161602 -59.711037
sto_xyz:3 -0.000068 -0.161602 0.986856 -2.379487
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
~~~
qform_code=0 means that the physical coordinate system is should not be considered (see ["METHOD 1" in nifti doc](https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html)), and that some software will consider the sform instead.
I _think_ we should set the qform_code=1 for our testing data, because this is how we expect NIFTI header to be presented to SCT's functions.
Related to:
- https://github.com/sct-data/sct_testing_data/issues/5
- https://github.com/neuropoly/spinalcordtoolbox/issues/3283
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Research direction
Start by running fslhd on data_testing/sub-unf01/anat/sub-unf01_T1w.nii.gz and review the linked issues for the expected NIfTI header convention. Done means the testing data has qform_code=1 while retaining the stated coordinate information.
Written by the indexing model from the issue text.
Assessment
- Domain
- testing
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100