PV6 VisuSubjectType is not used to provide proper orientation in combination with VisuSubjectPosition

[gdevenyi]

In the case of PV6, there are several options for input subject type:

When combined with VisuSubjectPosition, these need to properly orient the scan in standardized coordinates.

Take for example a primate in "Head First Supine" vs a Rodent in "Head First Supine", the brain will be rotated by 90 degrees relative to each other.

This will also probably require some special casing for PV5, as it does not seem to have an option to set this parameter and always specifies SUBJECT_type=Human

[dvm-shlee]

@gdevenyi It actually integrated but just not thoroughly tested, so I'm not sure it works correctly,
Currently, I only have a dataset with Quadruped but apply -90 degree on X-axis and 180 degrees for Y-axis to correct the orientation for Biped. (For Quadruped - Head_Supine is located 180degree for Z-axis, so I think overall the result is the same as you suggested). Not sure the PV6 handle 'OtherAnimal' differently, because I was only able to find Biped and Quadruped from the 'VisuSubjectType' metadata field so far (from the manual).
The code is located at brkraw.lib.utils.build_affine_from_orientation_info
In case this is not functioning as you expected, could you provide any sample that shows the issue?

[gdevenyi]

Ah sorry, I see you have some corrections. I've gotten confused as the scanner console does not have the same options as the code and I was searching for the scanner options in the source.

I think for Other (and maybe Phantom) no correction should be applied? I'm pretty sure the orientation settings are disabled at the console. As for OtherAnimal, at least for their example a snake has the same brain-to-body geometry as a quadruped.

As I mentioned elsewhere I'm collecting a complete dataset of a phantom with all the various settings flipped around in combinations to test all configs.