Problem finding T2w images

[joebathelt]

Describe the bug
I'm trying to run BIDSonym on a dataset that contains T1w and T2w images. The dataset is organised according to BIDS 1.9 and passes the BIDS validator test, both with the current version of the validator and the one inside the BIDSonym container. fMRIPrep also worked with this dataset and used the T2w image as expected. However, with BIDSonym, the defacing of the T2w images files fails with an error indicating that they cannot be found: Exception: You indicated that a T2w image should be defaced as well.However, no T2w image exists for subject 001 and indicated sessions.Please check again.

To Reproduce
Organisation of the BIDS dataset (omitting additional runs and other participants):

├── sub-001
│   ├── anat
│   │   ├── sub-001_T1w.json
│   │   ├── sub-001_T1w.nii.gz
│   │   ├── sub-001_T2w.json
│   │   └── sub-001_T2w.nii.gz
│   ├── fmap
│   │   ├── sub-001_dir-PA_run-1_epi.json
│   │   ├── sub-001_dir-PA_run-1_epi.nii.gz
│   └── func
│       ├── sub-001_task-raven_run-1_bold.json
│       ├── sub-001_task-raven_run-1_bold.nii.gz
│       ├── sub-001_task-raven_run-1_events.tsv

Code to run BIDSonym:

docker run -i --rm \
           -v /home/shared/intrainter/data/export_bids:/bids_dataset \
           peerherholz/bidsonym:latest \
           /bids_dataset group --deid pydeface \
           --deface_t2w \
           --brainextraction bet \
           --bet_frac 0.5

I also tried this with mri_deface and go the same issue:

docker run -i --rm \
           -v /home/shared/intrainter/data/export_bids:/bids_dataset \
           peerherholz/bidsonym:latest \
           /bids_dataset group --deid mri_deface \
           --deface_t2w \
           --brainextraction bet \
           --bet_frac 0.5

Expected behavior
I expected BIDSonym to find the T2w image.

OS/environment (please provide precise information on your OS/environment):

• Docker: 27.3.1
• OS: Ubuntu 22.04.5 LTS