Hi Päivi,
You can use the fslswapdim command:
fslswapdim input.nii -x y z output.nii
Unfortunately this problem will possibly occur whenever you copy data
between between FSL and Matlab, so make sure to look at your data.
Cheers,
Paul
On Wed, 28 Nov 2018 at 15:54, Paivi Eerola <[log in to unmask]> wrote:
>
> Please, ignore my previous message. I managed to fix the coordinate system by using the command you gave me fslcpgeom.
> Interestingly, I am seeing now the NII flipped along the X axis. The blobs that I know are left hemispheric, appear on the right hemisphere. What is happening?
>
> Thanks!
> Päivi
>
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