Hi AFNI experts!
I tried to extract brains from MPRAGE images within AFNI using 3dIntracranial and I do not get good results. Therefore, I had to change manually the defaults of 3dIntracranial, which improved the results a bit. However, a rather time consuming manual editing procedure with the drawing plug in was necessary and I got a little tired of it.
Therefore, I tried brain extraction with Freesurfer and BET and results looked amazingly good. However, the orientation changed, when I tried to convert these images back to AFNI BRIK format and it seems that I lost on the way the information of the original position and orientation of the head, which I need to do a good nudging with 3dAnatnudge.
It would be very helpful, if anybody could tell me, how I could re-apply the spacial information of the original head BRIK file to the brain extracted BRIK file derived from ANALYZE (BET) or COR (Freesurfer) files.
Thanks,
Lukas
