I think your mprage image was taken in the sagital view.
You will need to re-orient the mprage image before any spatial registration, otherwise, you will get a distorted brain.
I know two ways to correct the orientation:
1. Use MRIcro [go to "file" --> save as (rotate/clip/format...)] --> then choose format to "sagittal-left".] However, you will need to do one by one using this method. 2. Use fslswapdim, you can try and error to find the correct combination of xyz, i think you will need something like -z x y, not sure.
Yi-Shin
On Mon, Mar 30, 2009 at 7:40 PM, Gregg DiGirolamo <[log in to unmask]> wrote:
I'm having the same problem, and when I try to use Feat to register the anatomy, it confuses
the saggital with coronal, etc.
Mark said it was just a question of display, but the registations aren't working.