Update to use bl2bids

[soichih]

@faskowit

As we've been discussing on https://github.com/brainlife/brainlife/issues/43 .. I've updated app-fmriprep (master branch) to use the new bl2bids command to organize input data into bids, and while working on this I've also updated the fmriprep version to 20.1.1.

I've tested it with a few of my test cases, but I am sure there are other bugs still hidden somewhere. Can you help run some tests on the app-fmriprep master branch? (both the surface and volume version).

[giulia-berto]

I did a couple of tests and they finished successfully, both with the surface and volume versions. If you can update the docker to version 20.1.2 (last version) I may try also with that.

[soichih]

@giulia-berto I've updated master branch to use 20.1.2. I think the errors I've seen so far can only manifest on some input data, but not all(?). You should have read/write access to the repo, so please feel free to make any changed necessary (or send PR, either way is fine).

[faskowit]

Cool cool thanks for testing it out. We should keep our eyes on the fMRIPrep repo... the LTS release has a release candidate out right now. This seems like an excellent opportunity to hammer out and take care of errors... and keep it pinned at the LTS release.

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On Tue, Sep 15, 2020 at 10:28 AM Soichi Hayashi ***@***.***> wrote: @giulia-berto <https://github.com/giulia-berto> I've updated master branch to use 20.1.2. I think the errors I've seen so far can only manifest on some input data, but not all(?). You should have read/write access to the repo, so please feel free to make any changed necessary (or send PR, either way is fine). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZHY5BWQ345VKM6MTYSHUDSF52YJANCNFSM4PIK25UQ> .

[giulia-berto]

great, thank you @soichih!

I see, so @faskowit do you think we should try testing the version 20.2.0rc0?