Dear Afni experts,
I am trying to align EPIs of a brain that was scanned in 2 different session. The EPIs of the two sessions have the exact same acquisition grid dimensions, and the same position relative to the brain, since they were prescribed with autoalign on a Siemens scanner. So the brain position is well matched in the two image grids, and this is all I want because one of the things I ultimately want is to correct for residual distortions between-session in the phase-encoding direction only. But then, as I want to apply all rigid-body motion corrections and warps in one step with 3dNwarpApply, the fact that the position of the EPIs in scanner space don’t match (the head of the subject was not in exactly the same position relative to the bore) complicates everything (at least for me). After trying a lot, I feel I could accomplish everything easily if only I could fake that the scanner-space position of the second-session grid to be the same as that of the first-session grid. Then it would be just as if both set of EPIs were acquired in a single series of runs repeated in one session.
So the question is: do you have any tool or suggestion of a tricky trick that could change the header information of an EPI such that the scanner-space position of the grid would be the same as the scanner-space position of another EPI that has the same grid dimensions but different position?
Thanks a lot for your help and
Have a very good day!
Sébastien Proulx, MSc, PhD candidate