If you modify the line in $FSLDIR/bin/easythresh reading:
SM=`${FSLDIR}/bin/smoothest -z $1 -m $2`
to
DOF=`stats/dof`
SM=`${FSLDIR}/bin/smoothest -d $DOF -m mask -r stats/res4d`
Then that should get the results closer - note that this assumes the script will be run in the relevant FEAT directory, since the paths to dof/mask/res4d are relative.
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 15 May 2019, at 15:17, Leslie Cao <[log in to unmask]> wrote:
>
> Thank you, Matthew. That explains a lot. Is there a way to feed the smoothness file to easythresh so it can produce the same result as the Feat post-stat GUI?
> Thanks,
> Wen
>
> On Wed, May 15, 2019 at 8:04 AM Matthew Webster <[log in to unmask]> wrote:
> Dear Wen,
> Without looking at the exact calls, I would suspect that this difference may arise from the difference in how data smoothness is estimated - in the GUI pipeline ( FEAT? ) the smoothness is estimated from the residuals, while in easythresh it is estimated from the stat itself. Without knowing the ground-truth result, generally the FEAT results would be expected to be more accurate.
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 14 May 2019, at 16:28, Leslie Cao <[log in to unmask]> wrote:
>>
>>
>>
>> ---------- Forwarded message ---------
>> From: Leslie Cao <[log in to unmask]>
>> Date: Wed, May 8, 2019 at 3:40 PM
>> Subject: cluster correction using easythresh and GUI
>> To: FSL - FMRIB's Software Library <[log in to unmask]>
>>
>>
>> Dear FSL experts,
>> I am working on the cluster correction of an interaction image and found different results using easythresh and GUI. If I corrected the image at 3.1 0.01 in the GUI, there is nothing significant. However, if I correct the same zfstat image using easythresh at 3.1 0.01, I got two significant clusters. Is there an explaination for why this happened? Is the easythresh version valid?
>> Thanks,
>> Wen
>>
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