Originally posted by Pravesh Parekh: In NIFTI header there are three vectors:
float srow_x[4] ; /*!< 1st row affine transform. */
float srow_y[4] ; /*!< 2nd row affine transform. */
float srow_z[4] ; /*!< 3rd row affine transform. */

These are set by acpcdetect.  

NIFTI defineds the x,y,z directions as:
+x = Right +y = Anterior +z = Superior

Let's say (i,j,k) are the coordinates of the AC as detected by acpcdetect, they to get the transformed AC location you will perform the 
following:

x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]

Since you chose -center-AC option, the (i,j,k) of the AC locations should map to point (0,0,0), the center of the FOV of the transformed image.

Hope this helps.

Babak

P.S.  I should add that since in acpcdetect V2 the transformation is further adjusted using the 8 Orion landmarks, AC may not be mapped exactly to (0,0,0) by the above formula, but it will be close.  To map the AC exactly to (0,0,0) you should use the -standard option as well, that is:

 acpcdetect -i filename.nii -no-tilt-correction -center-AC -noppm -nopng -v -standard