While testing different settings of sct_register_to_template to register T2*w axial image to the PAM50 template, I discovered that -ref subject preserves spinal cord anatomy, but -ref template does not.
Comparison (notice the changed SC shape/anatomy for the -ref template):
The main difference between -ref subject and -ref template is that within the -ref template, the straightening of the spinal cord is done (see the help of sct_register_to_template for details).
To verify if the straightening causes the anatomy alteration, I run sct_straighten_spinalcord:
Description
While testing different settings of
sct_register_to_template
to register T2*w axial image to the PAM50 template, I discovered that-ref subject
preserves spinal cord anatomy, but-ref template
does not.-ref subject
-ref template
Comparison (notice the changed SC shape/anatomy for the
-ref template
):The main difference between
-ref subject
and-ref template
is that within the-ref template
, the straightening of the spinal cord is done (see the help of sct_register_to_template for details).To verify if the straightening causes the anatomy alteration, I run
sct_straighten_spinalcord
:And indeed,
sct_straighten_spinalcord
modifies the spinal cord anatomy:Steps to Reproduce
Example T2*w data: t2s.zip
Thanks @sandrinebedard and @jcohenadad for the cooperation!