[feature proposal] BIDS directory as input

[neurorepro]

Hello,

Would it be of interest to add a feature so that pydeface accepts a BIDS directory as input, to make pydeface potentially run as a BIDS app ?

Many implementations are possible, with one possible first iteration e.g. relying on pybids and involving as parameters:

• a path to a BIDS directory
• an optional subject (all by default)
• an optional suffix (T1w by default)

Best practice seems to be replacing the original file with the defaced one so the output could be:

• the original non defaced file renamed as ..._desc-nondefaced_..._<suffix>.nii.gz
• saving the defaced file with the name of the original one (or e.g. ..._desc-defaced_...<suffix>.nii.gz)

[poldrack]

sounds like a great idea to me! probably need to think about how to handle cases where there is already a _desc- flag.

[ofgulban]

@neurorepro feel free to do a pull request. If you decide to do so, please ensure that your changes do not alter the current default behavior.

[neurorepro]

@ofgulban Sure, I will work on it and do a PR (everything backward compatible of course !)

[ofgulban]

saving the defaced file with the name of the original one (or e.g. ..._desc-defaced_...<suffix>.nii.gz)

This seems to have been discussed at #36 , maybe have a look there.

[neurorepro]

@ofgulban It could be temporarily included in the sidecar json as mentioned in #36.

Also a solution (hopefully soon fully BIDS compatbile) for the case @poldrack mentioned when a desc label is already present is to concatenate values with + as alluded to here

[effigies]

Note that https://github.com/PeerHerholz/BIDSonym wraps pydeface in a BIDS app that allows you to select your defacing method. Seems like it might be unnecessary effort building pydeface out into a BIDS app.

[neurorepro]

Hi @effigies , yes we saw that repo but it is no longer maintained

[effigies]

Oh. I was under the impression it was. cc @peerherholz for clarification.

[neurorepro]

I think it is also harder to maintain an aggregated tool depending on four defacing utilities than a single defacing utility.

By no longer maintained, i meant no actively maintained (the last commit is from 2021).

[neurorepro]

If it is deemed unnecessary to add BIDS app functionality to pydeface and @PeerHerholz's BIDSonym is actively maintained, then we will simply use BIDSonym

[PeerHerholz]

Ahoi hoi folks,

thx @effigies for the tag!

@neurorepro is definitely right in that BIDSonym is not really actively maintained, as I don't have time and funding to do so for a while now. The basic functionality is still working ok (I use the latest version quite often.) but it could for sure need a few updates here and there. I'm of course happy to support respective endeavors!

Cheers, Peer

[neurorepro]

Thank you @PeerHerholz for your feedback.

Then @effigies do you think it can be useful to add a BIDS app functionality to pydeface ?

[effigies]

Fine by me. I'm not maintaining here...

[ofgulban]

@neurorepro , looking at the latest commits, it seems that I am the one who is maintaining here. I would be curious to see a PR, but also at the same time worried if it is a big one (conference season is coming with work piling up). So my suggestion would be to maybe if possible start with something small but does what you wanted. I have to say that I am not familiar with the full extend of what "BIDS app functionality" means. I generally have two main worries:

• Breaking backwards compatibility
• Increasing the cost of maintenance in the long term (i.e. a lot of added lines of code)

So if you can address these, I would be happy to go through a PR.

[neurorepro]

@ofgulban sure, BIDS app functionality would mean having it BIDS-aware, i.e. run on a BIDS dataset without having to tell it where is the anatomical data (because BIDS does that)

[ofgulban]

@neurorepro that sounds cool and useful so that's fine with me.

[Remi-Gau]

am quickly trying to see if I can build a functional image of bidsonym that would have the latest version of each defacing tool... just in case this can avoid some wheel reinvention

[Remi-Gau]

I did not get super far but in case someone has some ideas, I am leaving this in a PR: https://github.com/PeerHerholz/BIDSonym/pull/70