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Dear Mark,
The image is not in MNI space.
Actually I want to work in original image space only.

Can you also tell me how to flip image along x axis which is in NEUROLOGICAL orientation.
Actually i tried with fslswapdim but it is giving error.


fslorient test_0001
NEUROLOGICAL

fslswapdim test_0001 RL PA IS test_0001_flip
Cannot perform requested swap (NEUROLOGICAL/RADIOLOGICAL storage inverted)
Try the following command instead:
fslswapdim test_0001 LR PA IS test_0001_flip.


Thanks & Regards.


On Thu, Jan 8, 2015 at 2:51 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

I¹m not entirely sure what you are asking here.
Do you want to flip the brain left-right and then subtract the original
from the flipped version?

If the brain is already in MNI space then the flipping is easy with
fslswapdim with the options -x y z.  If it not in MNI space then it is
more difficult, but let us know more about what you want to do and whether
your images are in MNI space or not.

All the best,
        Mark



On 05/01/2015 08:45, "SUBSCRIBE FSL Anonymous" <[log in to unmask]>
wrote:

>Dear FSL Experts,
>
>I want to separate left and right hemisphere of brain image in all the
>slices and then want to subtract them.
>Please suggest how can this be done in FSL.
>
>Thanks & Regards