Mriqc nipype.utils warning

Hello,
I’m just getting mriqc running using singularity, and although it provides output just fine for single subjects, I keep getting the following nipype.utils warnings after it starts running (initial command followed by initial output). I’m using Centos7 and just set this up a couple days ago so have the latest version of mriqc. Not sure if it matters, but my python default version is Python 2.7.5 because the yum installer on Centos 7 needs it to be this for it to work. Any ideas on how to stop these warnings? Thanks!!

[myID@mycomputer ~/]$ singularity run --cleanenv /home/mriqc_latest.simg /home/myID/TPC_Project/bids /home/TPC_Project/fmriprep_output/sub-tpc004/mriqc participant --participant_label tpc004

200717-19:36:51,529 cli IMPORTANT:

Running MRIQC version 0.15.2:
  * BIDS dataset path: /home/TPC_Project/bids.
  * Output folder: /home/TPC_Project/fmriprep_output/sub-tpc004/mriqc.
  * Analysis levels: ['participant'].

200717-19:36:51,822 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:36:52,54 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:04,646 cli WARNING:
IMPORTANT: Anonymized quality metrics (IQMs) will be submitted to MRIQC’s metrics repository. Submission of IQMs can be disabled using the --no-sub argument. Please visit https://mriqc.readthedocs.io/en/latest/dsa.html to revise MRIQC’s Data Sharing Agreement.
200717-19:37:26,925 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:26,950 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:26,954 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:26,966 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:26,980 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:26,983 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:26,991 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:27,16 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:27,27 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:27,34 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:27,37 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made
200717-19:37:27,128 nipype.utils WARNING:
Could not check for version updates:
Connection to server could not be made

1 Like

Ahoi hoi @Jeremy_Purcell,

thank you very for much for your post!
As you might be aware: this warning is related to nipype, mriqc’s underlying workflow engine and not mriqc itself. Introduced in nipype version 1.2.3, an automated version check is conducted upon initializing nipype. You receive the warning as you’re running mriqc via a singularity image that doesn’t have the corresponding possibility to do so. Thus, you can ignore this error as it won’t affect your mriqc outputs or change the respective nipype configuration in nipype/utils/config.py.

HTH, cheers, Peer

2 Likes

Hi all,

I get a similar warning when trying to run the latest docker image (MRIQC version 0.15.2). Am I correct in assuming that the cause of this error is similar to the one from the singularity image and therefore it is safe to ignore it.

I am running MRIQC version 0.15.2 on OSX 10.14.6

$ docker run -it --rm -v /Users/…/analysis/MRI/BIDS:/data:ro -v /Users/…/analysis/MRI/derivatives/mriqc:/out poldracklab/mriqc:latest /data /out participant --participant_label 001 --ica --hmc-fsl --no-sub

201026-03:48:12,663 cli IMPORTANT:
	 
    Running MRIQC version 0.15.2:
      * BIDS dataset path: /data.
      * Output folder: /out.
      * Analysis levels: ['participant'].

201026-03:48:13,93 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:13,511 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:26,342 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:26,362 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:26,385 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:26,411 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:26,500 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made
201026-03:48:26,529 nipype.utils WARNING:
	 Could not check for version updates: 
Connection to server could not be made