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Hello,
	This should just be a difference between inclusive and exclusive thresholds ( if your image has an integer data-type you could confirm this by off-setting the intensity thresholds by 1 ).

Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

> On 12 Aug 2017, at 17:07, Antonios Konstantinos <[log in to unmask]> wrote:
> 
> Hello fsl users,   
> 
> I am trying to figure out why I get a discreapancy in the result of fslstats thresholding and 
> the fslmaths thresholding.  
> 
> Here is my example:
> 
> fslstats image.nii.gz -P 5 -P 95 # Give me the 5 and 95 percentiles of the image (for the non zero voxels)
> 6.000000 1220.000000
> 
> fslstats image.nii.gz -M -l 6 -u 1220 -M # Use these percentiles to threshold the image and calculate the new -M thresholded value and see how it differs from the non thresholded one.
> 492.315100 473.398263
> 
> 
> fslmaths image.nii.gz -thr 6.000000 -uthr 1220.000000 image_thresholded.nii.gz # Do now the same with fslmaths
> fslstats image_thresholded -M #Calculate the new -M value
> 439.634478  # I was expecting that this value would be 473.398263 as fslstats gave.
> 
> What am I missing here?
> Thank you