Module QC failed

[zhaopluseins]

Dear Micapipe developers,

I tried to run micapipe on sub-HC001 in MICs dataset, and used commands same as the example. All status seemed to be completed, but all QC reports except "proc_structural" failed to be generated.

env info: Win11, WSL2, Ubuntu 22.04.3 LTS, Docker 26.1.0

How can I fix this? Thank you.

[araikes]

What was your call?

[zhaopluseins]

mridir=/mnt/e/test/mri
fslic=/mnt/d/software/wslinux/FreeSurferLicense.txt
bidsdir=${mridir}/bids
mriqcout=${bidsdir}/derivatives/mriqc
mriqcwork=${mridir}/mriqc_work
micapipeout=${bidsdir}/derivatives/micapipe
micapipetmp=${mridir}/micapipe_tmp
for subid in HC001
do
    docker run -it --rm -v ${bidsdir}:/bids:ro -v ${mriqcout}:/out -v ${mriqcwork}:/work \
    nipreps/mriqc:latest /bids /out participant --participant-label ${subid} --session-id 01 \
    -w /work --species human --no-sub --notrack --verbose-reports -m T1w dwi
    docker run -it --rm -v ${bidsdir}:/bids:ro -v ${micapipeout}:/out -v ${micapipetmp}:/tmp -v ${fslic}:/licence \
    micalab/micapipe:v0.2.3 -bids /bids -out /out -tmpDir /tmp -sub ${subid} -ses 01 -threads 12 -fs_licence /licence \
    -proc_structural -proc_surf -freesurfer -post_structural \
    -proc_dwi -SC -proc_func -GD -MPC -QC_subj
done

[araikes]

Do all of the outputs appear to be there? For instance, is /out/freesurfer populated?

Other things:

1. Do your DWI files match exactly the naming convention expected by micapipe? You may need to pass the path to the input files.
2. Same with fMRI files

[zhaopluseins]

Thank you for you reply. I checked output folder and there do exist some files, but I'm not sure whether they are entire. I used MICs example dataset so I think all files match the micapipe. (https://micapipe.readthedocs.io/en/latest/pages/04.databases/index.html#microstructure-informed-connectomics-mics)