Run fmriprep via docker gives error docker: invalid reference format


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.

Can you please provide the following information:

  1. What operating system you are running
  2. The full error log
  3. If data are BIDS valid
  1. That’s 145 GB! Do you really need that much?


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

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.

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