You can use fslmaths and the -thr option. This will exclude all values
less than (and maybe equal to) what you set as the threshold.
Example:
fslmaths tstat1.nii.gz -thr 2.5 tstat1_thr_2.5.nii.gz
Hopefully this is more what you were looking for,
Jacob
> Thank you for your reply Jacob, but just saving the command won't suffice
> for what I want to do with this thresholded image later. Basically, once I
> figure out a way to save the thresholded image, I want to separate this
> image into different ROIs. So I was going to multiply anatomical ROIs
> derived from the Harvard Oxford atlas with the thresholded image to get
> areas of significant intensity by region.
>
> So for this reason, I need to be able to get a saved thresholded image.
>
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