orientation information is contained in the dicom header. i will assume you have converted to nifti. if this information is incorrect (check with fslhd), you will have to to manually correct each individual brain. by that i mean create a new header for each image with fslcreatehd with correct orientation information.
good luck--christine
> Date: Mon, 22 Oct 2012 03:32:10 +0100
> From:
[log in to unmask]> Subject: [FSL] Orienting a brain
> To:
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> Hello,
>
> Is there a tool in FSL to orient the brain into standard space coordinates? Without normalizing the brain, keeping it in native space.
>
> Thank you very much,
