Jan Valosek

Just for clarification (I am the author of the original issue https://github.com/sct-pipeline/gm-challenge/issues/77); I did not work with PAM50 labels. Instead, I segmented the SC and GM using `sct_deepseg_sc` and `sct_deepseg_gm`...

The same sform and qform mismatch also occurred in `sub-10` and `sub-16` from the `dcm-zurich-lesions` dataset. I used the following fix: ``` sct_image -i sub-10_acq-ax_T2w.nii.gz -set-qform-to-sform sct_image -i sub-16_acq-ax_T2w.nii.gz -set-qform-to-sform...

@naga-karthik and @sandrinebedard experienced the same `raise ValueError("Image sform does not match qform") ValueError: Image sform does not match qform` error also for some subjects from the `spine-generic multi-subject` dataset:...

> New repository created: [manual-correction](https://github.com/spinalcordtoolbox/manual-correction). To do: > > * Collect the different versions of the script in various repositories, and put each one, as-is, in a separate branch of...

Closing since we have introduced [spinalcordtoolbox/manual-correction](https://github.com/spinalcordtoolbox/manual-correction) repository including [manual_correction.py](https://github.com/spinalcordtoolbox/manual-correction/blob/main/manual_correction.py).

> Maybe @valosekj can help with this as he has extensive knowledge of SC anatomy Sure! Happy to help. I will check this issue more deeply soon.

Two initials observations: - [`PAM50/histology`](https://github.com/spinalcordtoolbox/PAM50/tree/master/histology) is misaligned relative to [`PAM50/template`](https://github.com/spinalcordtoolbox/PAM50/tree/master/atlas). See the example below - [`PAM50_200um_AVF.nii.gz`](https://github.com/spinalcordtoolbox/PAM50/blob/master/histology/PAM50_200um_AVF.nii.gz) (blue) is completely misaligned relative to [`PAM50_wm.nii.gz`](https://github.com/spinalcordtoolbox/PAM50/blob/master/template/PAM50_wm.nii.gz) (orange): - interpolation artifacts are presented outside...

I'm a bit confused. It seems that the files hosted on osf.io (https://osf.io/8k7jr), which were provided within the[ first comment of this issue](https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/2179#issue-415677815) are the same files as in [spinalcordtoolbox/PAM50/histology](https://github.com/spinalcordtoolbox/PAM50/tree/master/histology)....

## Copying the header (qfrom and sfrom) Just for the sake of curiosity, I tried to update `qfrom` and `sfrom` by copying the header from `template/PAM50_t1.nii.gz` to `histology/PAM50_200um_AVF.nii.gz`: ``` sct_image...

Based on the [_Template creation_ section](https://www.sciencedirect.com/science/article/pii/S1053811918320044?via%3Dihub#sec2.3) in [Duval et al. Neuroimage 2019](https://pubmed.ncbi.nlm.nih.gov/30326296/): > **Template creation.** Maps of axon morphometry at the downsampled 50, 100, and 200 μm resolutions were registered...