cannot find mriqc_wf

[Elisabeth Freund]

I have been getting an error message with mriqc and wanted to look into the working folder to figure out what is happening.

However, I could not find this folder anywhere. Am I doing something wrong? Here's the command I ran:

docker run -it --rm -v /mnt/data/BON_data/BON001/Study:/data:ro \

-v /mnt/data/BON_data/BON001/Study/derivatives/mriqc:/out \

nipreps/mriqc:24.0.0 /data /out participant \

--participant-label 900003 --no-sub -w /mnt/data/tmp

I checked /mnt/data/tmp, but it is empty. Also nothing in my derivatives folder. The log file references files inside /mnt/data/tmp, though.

I also ran the same with an earlier version of mriqc (22.0.6), which runs successfully (my error occurs on dwi images in the newer version, so this is not surprising), but also does not create a working folder that I can find.

I have also tried setting both output directory and working directory to something inside my home directory to make sure this is not a mount issue. Same pattern.

Any help would be greatly appreciated!

[Elisabeth Freund]

I stumbled upon a solution myself.

Looks like I needed to mount the working directory as a volume in docker before using it.

In case anyone else ever needs to understand this, my example command needs to be changed to this:

docker run -it --rm -v /mnt/data/BON_data/BON001/Study:/data:ro \

-v /mnt/data/BON_data/BON001/Study/derivatives/mriqc:/out \

-v /mnt/data/tmp:/wdir \

nipreps/mriqc:24.0.0 /data /out participant \

--participant-label 900003 --no-sub -w /wdir