Intermediate nodes in worfklow do not generate all the outputs (FSL First Level Analysis)


Hi everyone,

I am implementing a FSL First Level Analysis into a nipype workflow with the aim of being reutilisable in future studies by just inputing the data. The base code for one specific subject can be found in my github:

First Level Modeling (FSL) using a nipype workflow

Basically, this code that I share with you is an adaptation of the excellent notebook created by Chris Gorgolewski:

First and Second Level Modeling (FSL)

The results for the contrast maps are the same as those in Chris’ code, which indicates that the pipeline works well. However, in contrast to his case, when the FEAT node is run, no design matrix and design_cov are generated and this is a kind of information I would like to be able to retrieve. I’ve been struggling with this, but I can’t see where is the problem. What am I missing here? Any suggestion?

Thanks a lot in advance!

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By default, the outputs which are not passed on to further nodes are deleted or not saved. I’m not sure where this is documented in the main docs, but an explanation shows up in Michael’s nipype tutorial. If you want the design matrices saved, I think your options are to either pass them directly to your outputnode, or configure the relevant nodes to keep unnecessary output (there’s an example at the bottom of the linked page).

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Yes! that was it Patrick! You saved me a lot time figuring out what was the problem and made me learn a new thing. Many many thanks!

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