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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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Add excerpts of how to cite fmriprep *AND* dependencies #713

Closed oesteban closed 7 years ago

oesteban commented 7 years ago

Meanwhile we can't implement this in a dynamic fashion with duecredit, we need to credit the authors of the huge amounts of software that fmriprep uses.

Update the documentation with these literate descriptions of references.

effigies commented 7 years ago

If there isn't already such a list, we can use this comment to build a running list of tools and citations, when available.

Tool Link to code Citation(s)
recon-all https://doi.org/10.1006/nimg.1998.0395
bbregister
mri_robust_template
oesteban commented 7 years ago

Great idea. I escalated it to a wiki entry: https://github.com/poldracklab/fmriprep/wiki/Software-references

chrisgorgo commented 7 years ago

Great move turning this into a wiki!

effigies commented 7 years ago

Okay, I think the wiki page is complete.

oesteban commented 7 years ago

WOW

oesteban commented 7 years ago

I was thinking about this:

  1. Move the table to an rst file in /REFERENCES.rst in the repo.
  2. Replace the wiki with a call to include this file (I'm guessing this is possible, but haven't tried though).
  3. When fmriprep finishes, print the excerpt selecting the appropriate rows from the table in the /REFERENCES.rst file.

WDYT?

effigies commented 7 years ago

I think that could be reasonable... I'm not sure how non-trivial it will be to grab the table rows you want.

effigies commented 7 years ago

But we could annotate it as "This tool is only used if you use phdiff fieldmaps", etc. Because most tools will be hit by anatomical and bold. ICA-AROMA has a flag, so that's easy. And there are a couple things that will get excluded/included if STC or FreeSurfer get turned off, or fieldmaps on.

chrisgorgo commented 7 years ago

We need something that is a) well exposed (so part of the website) b) easy to include in the paper (so a whole paragraph that someone can copy, paste and optionally adjust. I'm afraid that if we just provide a list of papers to cite most people will not use it.

chrisgorgo commented 7 years ago

https://github.com/ANTsX/ANTs#boilerplate-ants