Hi Pierre,
Thanks a lot. I am sorry for replying so late.
You gave more explanations than I expected about using other transformations estimated for the T1-fMRI coregistration (great). However, I have 2 runs for each subject. In this case, how the frmi data are coregistered onto the structural image ? Does niak coregister T1 onto run1 first, then run1 onto run2 ? How can I reset the coregistration stage for the both runs ?
Finally, how to display the dependences between the stages, in order to select the one need to be restarted ?

Regards,
K.