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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

local variable 'T1_file' referenced before assignment #86

Open hugofluhr opened 1 month ago

hugofluhr commented 1 month ago

Describe the bug I get an error when trying to run via docker (latest version). It seems the T1_file variable is referenced before assignment

To Reproduce Here is the command I am using: sudo docker run -i --rm -v /home/ubuntu/data/bids/ds-learninghabits:/bids_dataset peerherholz/bidsonym /bids_dataset participant --deid pydeface --participant_label 01 --brainextraction bet --bet_frac 0.5 --skip_bids_validation

Expected behavior I would expect the above command to run without probem

Screenshots Output of the command: Some packages in this Docker container are non-free If you are considering commercial use of this container, please consult the relevant license: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence Traceback (most recent call last): File "/opt/miniconda-latest/envs/bidsonym/bin/bidsonym", line 33, in <module> sys.exit(load_entry_point('bidsonym', 'console_scripts', 'bidsonym')()) File "/home/bm/bidsonym/run_deeid.py", line 366, in run_deeid Input data will not be checked for BIDS compliance. Found the following session(s) for participant 01: ['1'] elif len(T1_file) == 1 and args.deface_t2w: UnboundLocalError: local variable 'T1_file' referenced before assignment

OS/environment (please provide precise information on your OS/environment): Running on a Ubuntu 22.04 virtual machine.

jamesrcoleman97 commented 1 month ago

I'm getting the same exact error message after running with the same input command. Any idea on what might be causing this @PeerHerholz