Hi DataLad Team,
I want to add an mriqc and fmriprep container to the pipeline subdataset of my superdataset using datalad containers-add on our lab server running Ubuntu 20.04.3 (multiple users within the lab, no HPC) and DataLad 0.15.3.
For mriqc, this works without problems pulling the image from singularity hub:
datalad containers-add mriqc --url shub://ReproNim/containers:bids-mriqc--0.16.1 --call-fmt 'singularity run --cleanenv -B "$PWD,/data/singularity/:/data/singularity/" {img} {cmd}'
After this, datalad containers-run works perfectly
datalad containers-run -m "run mriqc on sub-KUL001" -i "BIDS/sub-KUL001/*" -o "mriqc/*" -n pipeline/mriqc BIDS mriqc participant --participant-label KUL001 --verbose --verbose-reports --fd_thres 0.9
However, since I cannot find the latest or a recent fmriprep container on singularity hub, I tried to add the image from Docker locally
datalad containers-add fmriprep --url docker://nipreps/fmriprep:20.2.6 --call-fmt 'singularity run --cleanenv -B "$PWD,/data/singularity/:/data/singularity/" {img} {cmd} --fs-license-file "$PWD/{img_dspath}/license.txt"'
I first ran into errors with permissions, but after solving those the container was succesfully added and saved to my subdataset, albeit with the following kind of warnings during installation
2021/11/25 11:22:48 warn rootless{dev/agpgart} creating empty file in
place of device 10:175
However, when trying to run fmriprep from the container
datalad containers-run -m "run fmriprep on sub-KUL001" -i "BIDS/sub-KUL001/*" -o "derivatives/fmriprep/*" -n pipeline/fmriprep BIDS derivatives participant --participant-label KUL001 --fs-no-reconall --fd-spike-threshold 0.9 --dvars-spike-threshold 2 --verbose --output-spaces MNI152NLin2009cAsym:res-2 --ignore fieldmaps --use-syn-sdc
I got the following output (hence no fmriprep run)
subdataset(ok): BIDS (dataset)
subdataset(ok): code (dataset)
subdataset(ok): derivatives (dataset)
subdataset(ok): mriqc (dataset)
subdataset(ok): pipeline (dataset)
subdataset(ok): sourcedata (dataset)
[INFO ] Making sure inputs are available (this may take some time)
[INFO ] == Command start (output follows) =====
WARNING: passwd file doesn’t exist in container, not updating
WARNING: group file doesn’t exist in container, not updating
INFO: No runscript found in container, executing /bin/sh
[INFO ] == Command exit (modification check follows) =====
action summary:
get (notneeded: 17)
save (notneeded: 7)
Do you have any suggestion on how to solve this? I guess datalad containers-remove and then datalad containers-add again from another location? Do you know of a singularity image for fmriprep 20.2.6 I can use for this purpose? Any other issues?
Thanks a lot in advance!
Best wishes,
Lukas