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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Move anatomical workflow out into niworkflows #881

Closed oesteban closed 5 years ago

oesteban commented 6 years ago

The anatomical workflow is mature enough to be detached from fmriprep's base code.

This would make the anatomical workflow more visible and will allow: 1) Move the anatomical workflow tests to niworkflows. 2) Cache all the anatomical workflow between circle builds (speed up build time of fmriprep).

WDYT?

(option 2 could happen before 1, that would also be okay)

effigies commented 6 years ago

I guess my question is whether it makes sense outside of fmriprep. As it is, we pipe a lot of options in through workflow arguments, which, on a first glance would seem to make it difficult to abstract to usability in another program.

oesteban commented 6 years ago

Let's start with 2 for now. I personally would have interest in seeing the anatomical workflows in niworkflows, but it is true that I know how to use them too well. Other users might be clueless.

oesteban commented 6 years ago

As we are considering to branch a dMRIPrep out, I guess this makes more sense now.

oesteban commented 5 years ago

See https://github.com/poldracklab/smriprep