The parameter in the second command is the 2nd percentile plus the difference between the 2nd and 98th percentiles ( here 8405 ) multiplied by the brain/background threshold ( here 10% ). Unless the 2nd percentile is unusually high, 10% of the 98th percentile will be a close approximation.

On 9 Apr 2018, at 10:15, Usman Ayub <[log in to unmask]> wrote:
Hi FSL experts,

As previously mentioned in another one of my emails (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;2f26d823.1803), I am writing an LPF script using log report of a FEAT GUI based HPF.

And I have a question, specifically related to this part of it:
...
/opt/fsl/fsl-5.0.9/fsl/bin/fslstats prefiltered_func_data -p 2 -p 98
2.000000 8407.000000 

/opt/fsl/fsl-5.0.9/fsl/bin/fslmaths prefiltered_func_data -thr 842.5 -Tmin -bin mask -odt char

/opt/fsl/fsl-5.0.9/fsl/bin/fslstats prefiltered_func_data -k mask -p 50
4573.000000
... 
Previously, I thought that the value of -thr parameter in the second command is actually 98th percentile value (as calculated in the previous command) divided by 10, but that turned out to be the case in only a few of the images.

So my question is, is this division by 10 a good enough estimate for this threshold or there is another way to calculate this value? if there is another way, can you please tell me how to do it?
Thanks,
Usman Ayub Sh