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spinalcordtoolbox / exvivo-template

High resolution ex-vivo MRI template of the cervical spinal cord.
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Should we reorient this template as RPI? #16

Open jcohenadad opened 3 years ago

jcohenadad commented 3 years ago

Currently, the template is oriented as LPI ("Neurological" convention). This has highlighted a problem when registering to a template https://github.com/neuropoly/spinalcordtoolbox/issues/3300.

Regardless this problem (which should be solved whatever orientation the template is), most templates are in fact RPI ("Radiological" convention), not LPI. Example:

So, it would be more consistent to keep with the convention.

Also see: http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm

charleygros commented 3 years ago

I think this has been fixed in a merged PR:

chgroc@rosenberg:~/exvivo-template$ sct_image -i template/exvivo_t2.nii.gz -getorient

--
Spinal Cord Toolbox (git-master-af2d4de531f66cd062af6fefa87c3f84185875ff)

sct_image -i template/exvivo_t2.nii.gz -getorient
--

RPI

Closing this issue.

jcohenadad commented 3 years ago

Reopening because fslhd says LPI (and I trust fslhd more than sct_image 😅 ):

 fslhd exvivo_t2.nii.gz 
[...]
qform_xorient   Left-to-Right
qform_yorient   Posterior-to-Anterior
qform_zorient   Inferior-to-Superior

version of the dataset: 6a595f97410f4a26882852fb6d1ab40389b78206

There might be a but in sct_image. Issue opened: https://github.com/neuropoly/spinalcordtoolbox/issues/3311