MRI-QC newbie question

1

Hello all,

new to MRIQC and unfortunately running into a probably very basic but still (for me) strange issue right at the start.
Habe a simple BIDS dataset with just two subjects to test (each only with a T1). BIDS validator says everything’s fine.

Running

docker run -it --rm -v /Current_Projects/mriqc/sample:/data:ro -v /Current_Projects/mriqc:/out poldracklab/mriqc:latest /data /out group

fails with these messages:

2018-07-16 09:31:02,783 mriqc.cli:WARNING No IQM-JSON files were found for the T1w data type in /out/derivatives. The group-level report was not generated.
2018-07-16 09:31:02,783 mriqc.cli:WARNING No IQM-JSON files were found for the bold data type in /out/derivatives. The group-level report was not generated.
2018-07-16 09:31:02,783 mriqc.cli:WARNING No IQM-JSON files were found for the T2w data type in /out/derivatives. The group-level report was not generated.
Traceback (most recent call last):
File “/usr/local/miniconda/bin/mriqc”, line 11, in
load_entry_point(‘mriqc==0.11.0’, ‘console_scripts’, ‘mriqc’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/mriqc/bin/mriqc_run.py”, line 387, in main
raise Exception(“No data found. No group level reports were generated.”)
Exception: No data found. No group level reports were generated.

Seems individual level fails (not generating IQM-JSONs) and thus group level fails.

Any thoughts?
Thanks!

2

Thanks for the info, I believe you are on the right track with your intuition about the files not being there for the individual participants.

Did you run this first?:

docker run -it --rm -v /Current_Projects/mriqc/sample:/data:ro -v /Current_Projects/mriqc:/out poldracklab/mriqc:latest /data /out participant

All I did was replace group with participant.

That command should generate the requisite files and then you can run the group command as you’ve written without error.

Best,
James

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3

Great James, that solved it. Error was lack of memory (had increased it from default 2 GB to 5.5 GB but that hadn’t been enough). Was warned when running participant level and then it worked after increasing RAM.

Thanks so much!

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