fully qualified streams

[Jonathan Peelle]

For one module I'd like to use epi images from a couple of stages back. I'm looking at:

https://github.com/rhodricusack/automaticanalysis/wiki/Stream-reference

and thinking I could fully qualify stream inputs based on the example. The example is:

<inputstreams>
    <stream>aamod_realign00001.epi</stream>
</inputstreams>

so if I want epis from the aamod_smooth stage, I would ask for aamod_smooth00001.epi as an input stream.

I can easily update the .xml header, or presumably the tasklist, to ask for this. But how do I handle this in the .m file? I don't want to change the .m file to get the aamod_smooth00001.epi stream instead of just 'epi' if I don't have to. Is there an elegant solution I'm missing?

I would also settle for a non-elegant solution I'm missing...

Thanks!

Jonathan

[Jonathan Peelle]

PS As an update, when including aamod_smooth00001.epi as an input stream in the XML file, I get an error because it's not an output of an earlier module, so I'm clearly missing something.

[Rhodri Cusack]

In the .m you can either ask for the fully qualified stream name (which is useful if there is more than one stream of this name) or just the regular stream name.

Let me know if this doesn't work - one of the updates might have broken it as it is a fairly irregularly used feature.

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