Hi Guangyu,

The non-256 version is already in MNI space. The 256 version is not.
For the non-256 version, FSLview shows the location of the crosshairs in MNI space.
If you are wondering how to relate a voxel in one of the image volumes of the IIT atlas (row x, column y, slice z) to MNI coordinates, then you simply need to multiply the following matrices:
[-1 0 0 90; 0 1 0 -126; 0 0 1 -72; 0 0 0 1] with [x y z 1]' , for non-256 image volumes of the IIT atlas.
or
[1 0 0 -128; 0 1 0 -145; 0 0 1 -109; 0 0 0 1] with [x y z 1]' , for 256 image volumes of the IIT atlas.
Please note that the x, y, z start at 0, not 1.

Regards,
Konstantinos