Hello Bianca,
                        -thr zeroes all voxels with an intensity below that of the threshold, e.g.

-thr 100

zeroes all voxels with a value below 100

-thrp calculates an intensity based on a percentage of the robust range ( essentially the 2%-98% range ) and zeroes all voxels with an intensity below that threshold

e.g.

-thrp 40

zeroes all voxel with a value below 40% of the robust range

-thrP calculates an intensity based on a percentage of the robust range of the non-zero voxels ( essentially the 2%-98% range ) and zeroes all voxels with an intensity below that threshold

e.g.

-thrp 40

zeroes all voxel with a value below 40% of the robust range of the non-zero voxels

In general, -thr is most useful when wanting to apply some absolute criteria to an image - e.g. thresholding a p-value image, while the percentile options are more useful for relative operations - e.g. removing the lowest 10% of voxels.

Hope this helps,
Kind Regards
Matthew


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

> On 22 Nov 2016, at 21:46, Bianca De Blasi <[log in to unmask]> wrote:
>
> Dear experts,
>
> could you please clarify on the fslmaths options: -thr, -thrp and -thrP. What is the difference between them and what are the cases in which one is preferred from the others?
>
> Sorry for this basic question but I could not find any example online.
>
> Thank you,
> Kind regards,
> Bianca