Bids app fails for me!
dnkennedy opened this issue · comments
I'm running the doceker bids app for antscortical thickness on Mac OSX (10.12.6).
Docker version: Version 17.09.0-ce-mac32 (19506)
My command was:
docker run -i --rm -v /Users/davidkennedy/Data/ABCDexample:/bids_dataset:ro -v /Users/davidkennedy/Data/antsoutexample:/outputs bids/antscorticalthickness /bids_dataset /outputs participant --participant_label A107 --n_cpus 3
After some time (~1 hour) , and lots of output to the screen, I get the following error:
ERROR: command exited with nonzero status 1
Command: /usr/lib/ants//antsBrainExtraction.sh -d 3 -a /bids_dataset/sub-A107/anat/sub-A107_T1w.nii.gz -e /opt/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz -f /opt/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumRegistrationMask.nii.gz -m /opt/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz -o /outputs/sub-A107/sub-A107_T1w_ -k 0 -s nii.gz -q 0 -u 1 -z 0
Traceback (most recent call last):
File "/opt/run.py", line 116, in
run(cmd, env={'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS': str(args.n_cpus)})
File "/opt/run.py", line 24, in run
raise Exception("Non zero return code: %d"%process.returncode)
Exception: Non zero return code: 1
Hi Dave!
I would need to see the "lots of output to the screen" to be able to triage this bug.
My best bet is that you run out of memory. You can control how much memory Docker on your mac has access to through Docker for Mac settings.
Hi Chris! Here you go with the gobs of output prior to death in a txt file. This text was preceded by the command I provided in the prior message and postceded by the afore mentioned error message:
Problem probably solved. More memory for Docker...