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

1

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

2

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:

1 Like
3

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

4

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

1 Like