Change2: new spherical coordinate definition in BRAINSCut

The previous formula were not correct, so they are modified based on
considerations on symmetric property of brain.
This is the second commit out of three:
As a short comment, here we have:
phi = arctan( |y|/x )
theta = arctan( sqrt( sqr(x)+sqr(y) ) / z )
More details can be found on Jira.
Change3: new spherical coordinate definition in BRAINSCut

The previous formula were not correct, so they are modified based on
considerations on symmetric property of brain.
This is the 3rd commit out of three:
As a short comment, here we have:

phi = arctan( |y|/x )
theta = arctan( sqrt( sqr(x)+sqr(y) ) / z )
phi = 180 - phi if phi>90
theta = 180 - theta if theta>90

More details can be found on Jira.