Hi AFNI experts,
I am confused about the mask coordinates. In Talairach space, locations in the left hemisphere have negative x coordinates, while locations in the right hemisphere have positive x coordinates. However, left/right coordinates seem to have been flipped in afni. For example, the Talairach coordinates of right Fusiform Face area were [-34.5, +43.5, -18.5].
Thanks a lot in advance.
Whenever you are talking about “coordinates”, it is not enough to report JUST the numbers. You also need to specify what order of coordinates you are using. There are two main ones in neuroimaging, popular with radiologists and neurologists separately:
- “RAI” order (also called DICOM order)
- “LPI” order (also called “SPM” order)
In RAI order, the “right” side values are negative (for the x-coord); the “anterior” side values are negative (for the y-coord); and the “inferior” side values are negative (for the z-coord).
In LPI order, the “left” side values are negative (for the x-coord); the “posterior” side values are negative (for the y-coord); and the “inferior” side values are negative (for the z-coord).
Neither is right or wrong, but this does mean that you ALWAYS need to report your ordering system along with coordinates. For example, state:
“Our magical point of activation in the brain is located at (-25, 16.3, 28) in RAI coordinates”; I can read that and see that the point is on the right, posterior and superior octant of the brain. In LPI coords, it would be at “(25, -16.3, 28)”.
For this very fun reason, the AFNI GUI also shows the L, R, P, A, I and S of a coordinate explicitly in the upper right of the main controller, to avoid ambiguity (you can switch using either RAI-- the default-- or LPI coords in your ~/.afnirc file; if you right click on the coords, you will get an option to change it just for that session).