Repositioning Structural MRIs to MNI space

Define the anterior commissure as the origin

Reorient images with anterior commissure as origin

• After the anterior commissure is defined, it's coordinates relative to the existing origin are found in the "Crosshair Position" box, defined in mm, for the x,y,z axes. For the the structural below this corresponds to [0.0 38.5 16.1]. [ ].
• Since we want to make the AC the origin, the image needs to be "shifted" by these values. Hence in the "right {mm}" box [ ] the value "0" is entered, in the "forward {mm}" the value "-38.5" and in the "up {mm}" box the value "-16.1" [ ].

attachment:spm1c.png Note that the sign of the values entered have the opposite sing than the ones in the Crosshair Position box. This is of course because the values in the Crosshair Position represent the differences between the current origin and the anterior commissure. Hence, after the anterior commissure is defined, the values entered in the "right", "forward" and "up" boxes should have the opposite sign than the ones in the Crosshair Position box.

Click the "Reorient Images" [ ]button and select the file with the structural image, which will then be reoriented.

To make sure that the process succeded, open the structural image again and click the the button underneath the "Crosshair Position" to move to the origin. If everything is correct the crosshairs will move to the anterior commisure and the xyz coordinates will be [0.0 0.0 0.0]