fMRIprep 1.2.4 running in local docker error

fmriprep

#1

I am trying to run the newer version of fMRIprep with one subject in the local docker with the command: fmriprep-docker --fs-license-file license.txt --cifti-output data/ds030-kevin output_60055 participant --participant_label 60055 but encountered an error after 13 hours in, with output ending with:

	 [Node] Finished "_gen_cifti0".
181205-23:02:52,111 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_60055_wf.func_preproc_task_rest_wf.gen_cifti".
Sentry is attempting to send 1 pending error messages
Waiting up to 2.0 seconds
Press Ctrl-C to quit
Captured warning (<class 'ResourceWarning'>): unclosed <socket.socket fd=5, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6, laddr=('172.17.0.2', 52540), raddr=('35.188.42.15', 443)>

Previously, I had no problem with running fMRIprep locally with an earlier version (I believe before 1.2.x). Are there any new set ups respectively? Thank you!


#2

Can you post the full log? There is no error in that excerpt. Thanks!


#3

Yes, I’ve pasted it in this doc (https://docs.google.com/document/d/1sYyMoIVoBUEv0_Q2mxG2sHerfKp_8UK0z4deRQm2vm8/edit?usp=sharing) due to the length of the log. Let me know if this helps!


#4

Thanks! I don’t see any errors, just a lot of warnings. Are you missing any of the expected outputs?


#5

My mistake… I’ve misread the output directory, so I do have the expected outputs. Thank you for the help and sorry about the confusion!