Hi,
In the 3drotate -help file it says :"if the realignment parameters are derived from a 3dvolreg run on a dataset with a different center in xyz space, the results may not be what you want".
I was wondering if this is because the realignment parameters in the output 1Dfile contain translational components correcting for the difference in position between the geometric center of the dataset (which is the origin about which the rotation is applied by 3drotate) and a presumed origin of the head rotation.
If so, how do you obtain the "real" origin of head rotation.

Is the specific center in xyz space that will be used for subsequent registration implicit in the 1Dfile output from 3dvolreg ? I guess it is not clear to me how a specific center (or origin) is associated with a 1Dfile.

The reason why I am asking this is because I am trying to use the 3drotate program to perform the registration of fMRI time-series using motion parameters obtained with an external monitoring device, and as you know, the origin about which to apply the motion (realignment) parameters is key to good registration.

thank you very much for your help,
Marleine