No disc levels in the AMU template: could be a problem

[jcohenadad]

consider adding a label files for disc levels

[vcallot]

Please consider adding the AMU7T_levels.nii as well (following our discussion .. and see amubox for downloads). Thanks!

[jcohenadad]

In nii.gz format 😊 , thank you

[Nilser3]

Thanks for this update @vcallot

Description

Currently the AMU7T template is using the PAM50_levels file for registrations, and now @vcallot provides us with a AMU7T_levels file.

AMU7T_levels.nii.gz header:

```console -- Spinal Cord Toolbox (6.2) sct_image -i AMU7T_levels.nii.gz -header -- sizeof_hdr 348 data_type UINT16 dim [3, 256, 256, 223, 1, 1, 1, 1] vox_units Unknown time_units Unknown datatype 512 nbyper 2 bitpix 16 pixdim [-1.0, 0.175781, 0.175781, 0.5, 1.0, 1.0, 1.0, 1.0] vox_offset 352 cal_max 0.000000 cal_min 0.000000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 toffset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Unknown qform_code 0 qto_xyz:1 -0.175781 0.000000 0.000000 22.425751 qto_xyz:2 0.000000 0.175781 0.000000 -69.173096 qto_xyz:3 0.000000 0.000000 0.500000 -193.340027 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -0.175781 0.000000 0.000000 22.425751 sto_xyz:2 0.000000 0.175781 0.000000 -69.173096 sto_xyz:3 0.000000 0.000000 0.500000 -193.340027 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 file_type NIFTI-1+ file_code 1 descrip aux_file ```

• AMU7T_levels is more adjusted to AMU7T template (see animation 1).

Animation 1: Comparison of PAM50_levels and AMU7T_levels

Experiments : Registration using each levels files separately

• Test subject: available https://github.com/spinalcordtoolbox/template_AMU7T/tree/main/code After a registrations using PAM50_levels and AMU7T_levels on the Test subject , results on animation 2:

Animation 2:

There is a better registration of AMU7T_levels mask.

Now, if we look at the template2anat files generated by using PAM50_levels and AMU7T_levels (see animation 3).

Animation 3:

I find small differences in the dorsal horns.

So I will create a PR to replace PAM50_levels by AMU7T_levels.