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PeerHerholz / BIDSonym

a BIDS app for pseudo-anonymization of neuroimaging data
https://peerherholz.github.io/BIDSonym/
BSD 3-Clause "New" or "Revised" License
51 stars 14 forks source link

Bidsonym not running #39

Closed araikes closed 3 years ago

araikes commented 3 years ago

Hi @PeerHerholz

I was trying to deface a dataset and I've run into an odd issue. I'm using the latest version (pulled the other day). This is what I get:

docker run -ti --rm -v /data/TBIMODEL_clean/nifti:/bids_data:ro peerherholz/bidsonym:latest /bids_data participant --participant_label UAHC101 --deid pydeface --brainextraction nobrainer
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.5.4

This dataset appears to be BIDS compatible.

        Summary:                   Available Tasks:                     Available Modalities:
        3402 Files, 20.27GB        rest                                 FLAIR
        161 - Subjects             TODO: full task name for rest        bold
        1 - Session                                                     events
                                                                        T1w
                                                                        dwi
                                                                        fieldmap
                                                                        fieldmap

        If you have any questions, please post on https://neurostars.org/tags/bids.

/opt/miniconda-latest/envs/bidsonym/lib/python3.6/site-packages/bids/layout/models.py:102: FutureWarning: The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
  FutureWarning)
Processing data from one session.

And there it stops. There's no error or anything. It just doesn't do anything and returns me to the prompt. I've tried it with different participant IDs as well as no :ro to no avail. Any thoughts?

araikes commented 3 years ago

As a follow up, I ran the same command on the same system with a longitudinal dataset and it works just fine (both group and participant analysis options).

araikes commented 3 years ago

Bump on this @PeerHerholz. Any idea why single session Bidsonym doesn't process the data?

PeerHerholz commented 3 years ago

Ahoi hoi,

as outlined in #40, this was related to a problem with how sessions were handled and fixed a while back, but corresponding changes were not pushed. This will happen asap.