I’ve been looking around for an explanation on what exactly the threshold input of the Nipype FILMGLS and FSL’s film_gls threshold input is about. For example, what units is it in? Is it for the pre-whitening or background? This becomes particularly important as I notice that fsl’s default is 1000 while Nipypes is 0. And I’ve seen codes with threshold = 10 in Nipype but also with threshold = 1000 (using SUSAN mask). For my own data, if I run it in Nipype with threshold = 1000 all copes and parameters end up empty as the numTS property in the FILMGLS logfile = 0. This data has already been processed through SPM and its more to test out nipype, so its not conceivable that no voxel passes a legitimate threshold.
So i’m wondering:
- What is the FILMGLS/ fls_gls threshold units and purpose?
- How is FILMGLS different from FSL’s film_gls terminal command if at all?
- Does the threshold unit’s meaning change depending on whether one is in native space or MNI/ Standard space? Currently I’m running FILMGLS on preprocessed native space.
Would appreciate your thoughts,