Weird warning: Quick validation failed - the general folder structure does not resemble a BIDS dataset

Hi experts!
When I am opening qsiprep with this following command:

docker run -ti --rm \
    -v $HOME/fullds005 \
    -v $HOME/dockerout \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    $HOME/fullds005 $HOME/dockerout participant \
    --ignore fieldmaps \
    --output-resolution 1.2 \
    --fs-license-file /opt/freesurfer/license.txt.

And qsiprep comes up with the following prompt:

Quick validation failed - the general folder structure does not resemble a BIDS dataset.
Have you chosen the right folder (with "sub-*/" subfolders)?
Check for structural/naming issues and presence of at least one subject.

But I have already verified that my data is in BIDS format using BIDS validator, so I would like to ask you experts what could be the problem? I would appreciate it if you can give me any reply!
Best wish!
Wang

Quick general questions:

  • which version of the BIDS validator did you use?
  • which version of qsiprep were you using?

Also when “mounting” your volumes, it is preferable to say “where” you are mounting them in your container.

I would try something like this where $HOME/fullds005 is mapped to /data/ and $HOME/dockerout is mapped /output/.

docker run -ti --rm \
    -v $HOME/fullds005:/data \
    -v $HOME/dockerout:/output \
    -v ${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    /data /output participant \
    --ignore fieldmaps \
    --output-resolution 1.2 \
    --fs-license-file /opt/freesurfer/license.txt.

See the nipreps doc for more hints:

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Thank you for your reply! The version of the BIDS is v1.14.0, and the version of qsiprep is 0.19.1.

Following your code, the BIDS problem has been solved, thank you for your reply again!

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