Windows powershell working environment error

I have given this command in windows powershell

PS C:\Users\axl666> fmriprep-docker .\Nifti .\Derivatives participant --participant-label sub-S0806 --fs-license-file .\license.txt --use-syn-sdc --output-spaces anat --stop-on-first-crash --fs-no-reconall --ignore slicetiming

And it shows the following error

fmriprep-docker : The term ‘fmriprep-docker’ is not recognized as the name of a cmdlet, function, script file, or
operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try
again.
At line:1 char:1

  • fmriprep-docker .\Nifti .\Derivatives participant --participant-label …
  • CategoryInfo : ObjectNotFound: (fmriprep-docker:String) [], CommandNotFoundException
  • FullyQualifiedErrorId : CommandNotFoundException

PS C:\Users\axl666> fmriprep-docker
fmriprep-docker : The term ‘fmriprep-docker’ is not recognized as the name of a cmdlet, function, script file, or
operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try
again.
At line:1 char:1

  • fmriprep-docker
  • CategoryInfo : ObjectNotFound: (fmriprep-docker:String) [], CommandNotFoundException
  • FullyQualifiedErrorId : CommandNotFoundException

Please help me in this

How did you install fmriprep-docker?

Hi Stevan,
Initially I have installed python and docker desktop and then after
I went t the site Docker Hub
and just copied this command in powershell
docker pull nipreps/fmriprep

So that is only installing the Docker container. fmriprep-docker is a wrapper function, which means it is a way to conveniently call fmriprep. However, fmriprep-docker needs to be installed, which you can do using pip install fmriprep-docker

I tried this also but same error

Does the pip installation proceed to completion?

Yes, It says its complete, but when I ask for fmriprep version nothing shows

you installed fmriprep-docker, so see if you you can run that.

Its says it is already installed

but nothing is working at all

Am I using correct command

PS C:\Users\axl666> fmriprep-docker .\Nifti .\Derivatives participant --participant-label sub-S0806 --fs-license-file .\license.txt --use-syn-sdc --output-spaces anat --stop-on-first-crash --fs-no-reconall --ignore slicetiming

Can you provide an error message?

fmriprep-docker : The term ‘fmriprep-docker’ is not recognized as the name of a cmdlet, function, script file, or
operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try
again.
At line:1 char:1

  • fmriprep-docker .\Nifti .\Derivatives participant --participant-label …
  •   + CategoryInfo          : ObjectNotFound: (fmriprep-docker:String) [], CommandNotFoundException
      + FullyQualifiedErrorId : CommandNotFoundException
    
    

PS C:\Users\axl666> fmriprep-docker
fmriprep-docker : The term ‘fmriprep-docker’ is not recognized as the name of a cmdlet, function, script file, or
operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try
again.
At line:1 char:1

  • fmriprep-docker
  •   + CategoryInfo          : ObjectNotFound: (fmriprep-docker:String) [], CommandNotFoundException
      + FullyQualifiedErrorId : CommandNotFoundException

I’m guessing python packages are not added to your path. Are you using python through Anaconda? Either way, if you have the docker container on your machine, you can alternatively call fmriprep through docker run (see below for an example)

so an example for you might be:

docker run -ti --rm \
    -v .\Nifti:/data:ro \
    -v .\Derivatives:/out \
    -v .\license.txt:/opt/freesurfer/license.txt \
    nipreps/fmriprep:latest \
    /data /out \
    participant \
    --use-syn-sdc --output-spaces anat \ 
--stop-on-first-crash --fs-no-reconall \
 --ignore slicetiming

I have added already pl check

I am used to dealing with python as part of an Anaconda installation, so I don’t know where the pip packages would be for a stand-alone python installation

I run the command that you give to me but again not working it says invalid

PS E:\test\S0806> docker run -ti --rm \ -v .\Nifti:/data:ro \ -v .\Derivatives:/out \ -v .\license.txt:/opt/freesurfer/license.txt \ nipreps/fmriprep:latest \ /data /out \ participant \ --use-syn-sdc --output-spaces anat \ --stop-on-first-crash --fs-no-reconall \ --ignore slicetiming

docker: invalid reference format.

See ‘docker run --help’.

PS E:\test\S0806>

Try putting quotes around “.\Nifti” “.\Derivatives” “.\license.txt”. Also I forgot the participant label argument but you can add that at the end. I am not a windows powershell user, but I imagine this might be due to how paths are coded differently in Windows vs Linux/Mac ("/" vs “\”).