[Freesurfer] aligning functionals to anatomicals

Hi,

I have a question regarding overlay of functional activations on a freesurfer map. After much work, I flattened my monkey brain. But, I just realized that the input volume , which I used to generate the flat maps, had orientation set to LIA. I want to over lay my functional activations, which are in RAS orientation on them. One way would be to realign all functional data into LIA orientation and then analyze the data and then simply use spmregister-see or fslregister-sess to register. Is there any simpler way?

My functionals are 65x85x56 for each slice. I tried using flirt to get the alignment matrix. But, it is failing badly.. Any ideas would be welcome..

Regards,

krishna