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bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer
Apache License 2.0
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License not being recognized... #39

Closed jlhanson5 closed 6 years ago

jlhanson5 commented 6 years ago

I was trying to test drive the BIDS freesurfer app, but couldn't get my license to be recognized.

My license exists as a file and is the new version (I'm using it for fmriprep... so I know it works/is valid). jamielh@pfc:~/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives$ ls /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives/license.txt /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives/license.txt

But this syntax: docker run -ti --rm -v /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1:/bids_dataset:ro -v /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives/freesurfer:/outputs bids/freesurfer /bids_dataset /outputs participant --participant_label NDARAA075AMK --n_cpus 2 --stages autorecon1 --steps cross-sectional --skip_bids_validator --license_file "/home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives/license.txt"

Leads to this error output: Traceback (most recent call last): File "/run.py", line 167, in <module> raise Exception("Provided license file does not exist") Exception: Provided license file does not exist

What am I doing wrong with that command line call? I tried with and without quotation marks, etc., but no luck. Thoughts?

chrisgorgo commented 6 years ago

You need to mount the license file with -v

docker run -ti --rm -v /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1:/bids_dataset:ro -v /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives/freesurfer:/outputs -v /home/jamielh/Volumes/Hanson/NKI_HealthyBrainNetwork/SI/R1/derivatives/license.txt:/license.txt:ro bids/freesurfer /bids_dataset /outputs participant --participant_label NDARAA075AMK --n_cpus 2 --stages autorecon1 --steps cross-sectional --skip_bids_validator --license_file "/license.txt"