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mtl-brainhack-school-2019 / matteo-mancini-trampolino

Diffusion meta-pipeline project for BrainHack School and the IronTract challenge.
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Alternatives to build pipelines for tractography #3

Closed matteomancini closed 4 years ago

matteomancini commented 5 years ago

@PeerHerholz given that you work with tractography, I wanted to ask if you actually have seen tools that allow you to build modular pipelines. So far, apart from what you can do with Nipype, I couldn't find anything specific, the only similar thing is TractoFlow, based on Nextflow, but it is more of a specific pipeline rather than a tool to implement several pipelines.

alexapichet commented 5 years ago

Highly recommend using TractoFlow if you want to preprocess your diffusion data!

PeerHerholz commented 5 years ago

Less "work", more "playing around", but nipype is a good starting point. It supports dipy to quite some extent. If you're interested in building modular pipelines, it would be cool to use niflows (intro here). There's also dmriprep which could be interesting. Porcupine within Giraffe tools could also be extended respectively.

matteomancini commented 4 years ago

@alexapichet thank you for the suggestion, I checked it out and it is interesting, I am thinking of implementing that pipeline in trampolino. @PeerHerholz niflows seems an ideal next step for my application, so definitely future work, thank you for the suggestion!