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Donders-Institute / bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS
https://bidscoin.readthedocs.io
GNU General Public License v3.0
130 stars 35 forks source link

Add citation information for plugin tools #208

Closed wtclarke closed 1 year ago

wtclarke commented 1 year ago

Please could you add citation information for the tools that act as plugins to bidscoin? Plugins like spec2nii, 'dcm2niix' and PET2BIDS request that users cite other outputs when used, however it's very easy for users to miss this when using tools, like bidscoin that wrap these other tools.

PET2BIDS citation info spec2nii citation info dcm2niix citation info

Would you consider listing these (and any others you know of) in the readme? Of course, with a note that they are only needed if certain functionalities are used. Do you also give citation information as an output to the user? I noticed something called duecredit in the source code. Is there a way that plugin developers can make this easier/automated for you?

marcelzwiers commented 1 year ago

I added a duecredit file myself for others to collect BIDScoin citations, but I don't create a duecredit report for the software that BIDScoin uses. Good point, I will implement that for the next release! For non-python tools, such as dcm2niix, I will add that manually. Will you add a due file for spec2nii (it's really easy, just add the file and import due.py e.g. in your main init.py file)?

marcelzwiers commented 1 year ago

I added a duecredit citation for dcm2niix and spec2nii (nibabel already has one and pet2bids is nearly dead). I was able to generate a duecredit report from the commandline (although somehow it didn't work for all bidscoin tools), but I failed to interface with duecredit directly from within BIDScoin. For more info on duecredit see:

https://github.com/duecredit/duecredit

marcelzwiers commented 1 year ago

Mhh, I'm giving it up, duecredit lost its credits with me. I'll think of another way to add references...

marcelzwiers commented 1 year ago

For now, I added a link in the README to the plugins page for further citation info: https://bidscoin.readthedocs.io/en/latest/plugins.html#dcm2niix2bids-a-plugin-for-dicom-and-par-rec-data

marcelzwiers commented 1 year ago

Ok, I got the duecredit lib to work, see: https://github.com/duecredit/duecredit/issues/188

I still don't know how to use it programmatically, but that will be for later

wtclarke commented 1 year ago

Hi @marcelzwiers ,

Thanks for the quick and positive response. Much appreciated. I'll take a look at the suggestion you made for spec2nii shortly.

Will