[DAT]: UCLA #88

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opened 2022-09-20 06:44:04 +00:00 by kaurao · 5 comments

kaurao commented

2022-09-20 06:44:04 +00:00

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Which dataset is it?

UCLA, already preprocessed and covers multiple diagnosis

Implementation

Did not implement anything

Your implementation

No response

Dataset access restrictions

Public and open access (no registration)
Public and open access (registration required)
Restricted access (needs approuval)
Available only in specific locations (Juseless, Jureca)

Anything else to say?

https://openneuro.org/datasets/ds000030/versions/1.0.0

### Which dataset is it? UCLA, already preprocessed and covers multiple diagnosis ### Implementation Did not implement anything ### Your implementation _No response_ ### Dataset access restrictions - [X] Public and open access (no registration) - [ ] Public and open access (registration required) - [ ] Restricted access (needs approuval) - [ ] Available only in specific locations (Juseless, Jureca) ### Anything else to say? https://openneuro.org/datasets/ds000030/versions/1.0.0

fraimondo commented

2022-09-20 06:49:37 +00:00

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Will be implemented for release

LeSasse commented

2022-10-05 17:45:33 +00:00

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I would be happy to look into it, if no one else is workimg on it yet?

🚀 1

fraimondo commented

2022-10-06 08:02:23 +00:00

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I would be happy to look into it, if no one else is workimg on it yet?

@LeSasse all yours!

> I would be happy to look into it, if no one else is workimg on it yet? @LeSasse all yours!

LeSasse commented

2022-10-06 09:44:41 +00:00

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Data available on openneuro (https://openneuro.org/datasets/ds000030/versions/1.0.0) is unfortunately version 1.0.0 which has no fmriprep derivatives that I would ideally like to use, so I found the old openfmri dataset hosted via datalad here: http://datasets.datalad.org/?dir=/openfmri/ds000030 Unfortunately, I think this one is version 1.0.3 which still does not contain the fmriprep derivatives. From what I can tell from the openneuro website, the fmriprep derivatives are contained in there from version 1.0.4 onwards and are available in an S3 bucket here: (https://legacy.openfmri.org/s3-browser/?prefix=ds000030/ds000030_R1.0.5/uncompressed/). I think with these data we can not use datalad.

Few options:

Somehow get an updated datalad dataset (remote or local)
make a class that can get S3 data
fmriprep data ourselves
leave the data out for now

LeSasse commented

2022-10-06 14:08:16 +00:00

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@fraimondo @kaurao During the datalad office hour I was told that the openneuro people are working on fmriprepping all the different datasets again, so Adina will let us know once our particular UCLA dataset is done. I suggest that we set up the datagrabber using the local data that @dlarabi has available in the meantime, and once the openneuro dataset is available we can integrate it using the remote dataset.