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Hi Martijn,
Well spotted! The subsample options do not interact with the kernel option ( we will updated the help text to make this clear ). You could use fslplit/fslmerge along with the fslmaths subsample option as an alternative processing method.

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 2 Jul 2018, at 13:05, Steenwijk, Martijn <[log in to unmask]> wrote:

Hi all,
 
I would like to subsample 2D data only in x-y plane. According to the help of fslmaths this can be done by using options -kernel 2D -subsamp2, but despite the kernel 2D – option the output is also subsampled in z-direction.
 
Any suggestions or alternatives?
 
Best,
Martijn 
 
 
 

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