Correct fMRI brain orientation

[bear_sun]

Hi,

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!
Best,
Liwei

[Steven]

@bear_sun

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?

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

[bear_sun]

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.