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add note for check orientation #211

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Jun 26, 2024
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add note for check orientation #211

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6 changes: 6 additions & 0 deletions docs/source/documentation/brainreg/user-guide/checking-orientation.md
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Expand Up @@ -16,3 +16,9 @@ Top is the reference atlas, averaged for all directions and bottom is the aligne
## Correct orientation
Top is the reference atlas, averaged for all directions and bottom is the aligned input data with correct input
![correct-orientation](../images/correct_orientation.png)

## A note about the camera position

In asymmetric cases (e.g. if you are registering to a single hemisphere or an asymmetric atlas), you may wonder about the camera position you are viewing the projections from. The origin of the projection image is at its top-left corner, the first axis runs top-down, and the second axis runs from left to right.

For example, if the atlas is ASR, projection 1 (along the S-I axis) will have the anterior-most, right-most (AR) point on the top-left, with the A-P axis running from the top to the bottom of the screen, and the R-L axis running from left to right. This means you are viewing the brain from "below" (from inferior to superior).