ivadomed / ivadomed/data-testing

qform=2 on testing data

Open
#12 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
No language data
Stars
1
Forks
1
PR merge metrics
No merged PRs in 30d

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

Contributor guide

No contributing guide indexed for this repository

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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.