threshold in `fsl.FILM_GLS`

[djarecka]

Summary

I'm wondering why the threshold trait for FILM_GLS for 5.07 (and 5.05) takes -1000 as default value. Is this just a typo?

motivated by this qst

[effigies]

Looks like it was introduced in #899 by @satra.

[satra]

in typical fsl processing the input time series to FILM_GLS is scaled to a median value of 10000. a typical threshold of 1000 represents 10% of this number, to remove background noise. why it was set to these specific numbers is historical and someone from FSL would have to answer that.

as of version 5.0.7, one could potentially send FILM_GLS a time series that was not scaled to 10000. since the band pass filter would not add the mean back. the default was set to -1000 to ensure that in such a situation one would still get an output.

in the poster's question, it would depend on the preprocessing performed. one option would be to calculate something like the 10th (not to confuse with 10 above) percentile of the timeseries and set the threshold to this value. leaving it as default should also result in a non-empty contrast.

[djarecka]

Thanks @satra for the explanation.

There is one other problem with syntax, that probably doesn't change too much in this case. So fsl.FILMGLS().inputs.threshold gives 0 as default value (not -1000), as in the poster's question.

I've been just checking this, and the problem is that we're using there default as a name of the argument, and in fact it is default_value. So traits simply takes its own default value for float if usedefault=True. In most places in nipype we don't name the argument, so it works ok.

[djarecka]

And if traits type is Range like here, value has to be used.