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:

--
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.