Correct fMRI brain orientation


I just got some fMRI data from a hospital, in which the doctor asked the patients to lay on their left sides while scanning for some reason. So it caused a problem in the original data: The LR is actually AP, while the AP is actually RL in the data. I am wondering if there is any way to manually correct this orientation problem with some software?

Thank you!

Hi Liwei, try reorient2std from FSL (described along with some other potentially useful functions here: Fslutils - FslWiki).

Thank you again, Steven. I tired a series of FSL functions (fslreorient2std, fslorient, fslswapdim etc.) and get confused what they were actually doing. So I ended up using Freeview - Tools - Transform Volumes to just rotate the whole brain physically by -90 degree along z (I-S) axis. Now it looks look for me.