Change oreintation in FSL

One of the useful function from FSL is fslswapdim, it can change the orientation of the image. Therefore, you can have the same orentation between T1 and T2 to run the further process.

let’s say you have a T2 image looks like this:

but the T1 image like this

So, you can want to change the orientation so that the T1 and T2 can match, type:

fslswapdim T2.nii.gz x -z y T2.reorientated.nii.gz

Now, you get the new orientated T2