defaced T1 file name

[Aaron Tanenbaum]

Hello Y'all,

I need to deface our T1s and T2s. I am looking up the common file name conventions. I need to keep the original file and the defaced file in the same directory. This is not my choice.  I saw a post online where I can add the entity acq-defaced to the file to signify it is defaced. Is this bids compliant. 

Thank you in advance.

[‪‪Dr Cyril Pernet‬‬]

Hi Aaron

The recommendation is desc-defaced as described here https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html

Note that while this is under the derivatives section, it also recommend to have this as raw, so no problem at all with the folder and files here. 

Best

Cyril 

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[Marcel Zwiers]

You can (mis)use the acq entity or better, you the json sidecar files as suggested here: https://github.com/poldracklab/pydeface/issues/36

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Op do 8 aug 2024 21:54 schreef Aaron Tanenbaum <aaron.b....@gmail.com>:

Hello Y'all,

I need to deface our T1s and T2s. I am looking up the common file name conventions. I need to keep the original file and the defaced file in the same directory. This is not my choice.  I saw a post online where I can add the entity acq-defaced to the file to signify it is defaced. Is this bids compliant. 

Thank you in advance.

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[Cyril Pernet]

yeah .. but that was before we merged the new(ish) desc-, so I'd recommend the latest bids version and have sub-xxx_use desc-defaced_T1w.nii and if you want to go further and use or create a mask you can also store that defacing mask (https://bids-specification.readthedocs.io/en/stable/glossary.html#defacemask-suffixes)

To view this discussion on the web visit https://groups.google.com/d/msgid/bids-discussion/CAK1xeXWN2oq_2v%2BjHFwfwHEut_%3DmAsu6XW0G42QjXfD7xY%3DGhA%40mail.gmail.com.

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-- 
Dr Cyril Pernet,
Neurobiology Research Unit
Copenhagen University Hospital, Rigshospitalet
Building 8057, Blegdamsvej 9
DK-2100 Copenhagen, Denmark

wamc...@gmail.com
https://cpernet.github.io/
https://orcid.org/0000-0003-4010-463

[yarikoptic]

FWIW +10 to Cyril's reply/advice -- `_desc-defaced` is IMHO how it should have been from day 0 of the BIDS which wanted to be "raw" whenever it was/is not ;)  and yes, then everyone would have just known either they are processing defaced or not image.

PS We will get more fun whenever we get some `_proc-defaced` as scanners would start defacing MRIs for us ;)