Open neurorepro opened 1 year ago
sounds like a great idea to me! probably need to think about how to handle cases where there is already a _desc- flag.
@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.
@ofgulban Sure, I will work on it and do a PR (everything backward compatible of course !)
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.
@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
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.
Hi @effigies , yes we saw that repo but it is no longer maintained
Oh. I was under the impression it was. cc @peerherholz for clarification.
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By no longer maintained, i meant no actively maintained (the last commit is from 2021).
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
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
Thank you @PeerHerholz for your feedback.
Then @effigies do you think it can be useful to add a BIDS app functionality to pydeface ?
Fine by me. I'm not maintaining here...
@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:
So if you can address these, I would be happy to go through a PR.
@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)
@neurorepro that sounds cool and useful so that's fine with me.
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
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
Hello,
Would it be of interest to add a feature so that
pydeface
accepts a BIDS directory as input, to makepydeface
potentially run as a BIDS app ?Many implementations are possible, with one possible first iteration e.g. relying on
pybids
and involving as parameters:T1w
by default)Best practice seems to be replacing the original file with the defaced one so the output could be:
..._desc-nondefaced_..._<suffix>.nii.gz
..._desc-defaced_...<suffix>.nii.gz
)