Run fmriprep via docker gives error docker: invalid reference format

alado · April 10, 2022, 5:49am

Hi!

I’m trying to run fmriprep directly via docker using command: docker run -ti --rm \ -v "/mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/Pilot/TUE009_PILOT04_TUE009_PILOT04/Nifti:/data:ro" \ "/mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/Pilot/TUE009_PILOT04_TUE009_PILOT04/preprocessed:/out" \ nipreps/fmriprep:latest \ --participant-label pilot4\ --fs-license-file /mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/license.txt \ --omp-nthreads 8 \ --nthreads 12 \ --mem-mb 145000 \ --low-mem \ /data /out \ participant

I tried also without " and , but it gives the error anyway.

Steven · April 10, 2022, 4:50pm

Can you please provide the following information:

What operating system you are running
The full error log
If data are BIDS valid

That’s 145 GB! Do you really need that much?

Best,
Steven

alado · April 10, 2022, 10:54pm

LInux
docker: invalid reference format. (that’s the entire error)
the data are in BIDS format
without this flag I’m anyway getting this error

Steven · April 10, 2022, 11:27pm

What is the output of ls /mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/Pilot/TUE009_PILOT04_TUE009_PILOT04/Nifti ?

Also there is not a space between the subject label (pilot4) and the following slash.

Finally, you should remove the quotes in the path arguments for -v, and make sure that EACH path you want to bind is preceded by -v.

Steven · April 10, 2022, 11:32pm

docker run -ti --rm -v /mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/Pilot/TUE009_PILOT04_TUE009_PILOT04/Nifti:/data:ro -v /mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/Pilot/TUE009_PILOT04_TUE009_PILOT04/preprocessed:/out -v /mnt/TUE_general/Projects/TUE009_DFG_Glucose_RPE/10_MRI/license.txt:/license.txt nipreps/fmriprep:latest --participant-label pilot4 --fs-license-file /license.txt --omp-nthreads 8 --nthreads 12 --mem-mb 32000 --low-mem /data /out participant