Registration using sct_register_multimodal gives a cropped result

[Nilser3]

Description

I have registered T2w images (fat-suppressed and non-fat-suppressed) from session 01 to session 02 using sct_register_multimodal (code here) with 3 strategies:

1. Rigid registration
2. Rigid + affine + syn registration
3. Rigid + affine + syn + dl registration

Also, there is a baseline registration that was made by the authors of the dataset, details (From here):

• Apply a centered transformation
• Apply a rigid transformation
• Apply a deformable transformation (B-spline) with Elastix using a preset parameter map (Parameter map 23 in the Elastix Zoo).

Then, when comparing the coregisters generated by sct_register_multimodal with the baseline, I observe that in all cases sct_register_multimodal gives us a cropped image (see animation).

QC of registration

• T2w non-fat-suppressed
• T2w fat-suppressed

Legend:

1. desc-registered_T2w.nii.gz -> baseline registration (made by dataset authors)
2. sct_rigid/...nii.gz -> Rigid registration using sct_register_multimodal
3. sct_syn/...nii.gz -> Rigid + affine + syn registration using sct_register_multimodal
4. sct_dl/...nii.gz -> Rigid + affine + syn + dl registration registration using sct_register_multimodal

[Nilser3]

Subjects registered with sct_register_multimodal produced in an empty image (see QC):

• T2w non-fat-suppressed
  sub-003 , sub-004 , sub-080

• T2w fat-suppressed
  sub-025 , sub-029 , sub-041 , sub-053 , sub-067 , sub-078 , sub-104 , sub-172 , sub-194 , sub-195