QSIPrep stagnate in the output of reconstruction report

When I run QSIPrep, everything seems good until the ConnectivityReport step. The message in the terminal shows that QSIPrep has already finished the step of “plot_connectivity”.

But nothing further happened. It stagnated at this step.

Now. this is all output files in my dwi directory of qsirecon.

This is my command:

qsiprep-docker /mnt/workdir/DCM/BIDS /mnt/workdir/DCM/BIDS/derivatives/qsiprep participant --participant_label 073 074 --output-resolution 2 --recon_input /mnt/workdir/DCM/BIDS/derivatives/qsiprep --recon_spec /mnt/workdir/DCM/Docs/Reference/qsiprep/mrtrix_multishell_msmt_ACT-hsvs.json --fs-license-file /mnt/data/license.txt --freesurfer-input /mnt/workdir/DCM/BIDS/derivatives/freesurfer -w /mnt/workdir/DCM/working --custom_atlases /mnt/workdir/DCM/Docs/Reference/qsiprep/qsirecon_atlases --nthreads 100 --gpus all

I’m not sure if qsiprep has finished its work because there were no errors in the terminal or the qsirecon directories. Can you please help me to confirm if it has completed its task?

I even can found the figures which should present in recon-report.

Hi @YukunQu,

Is there an HTML available for the subject? If so, that probably means it finished.


I suggest adding -v -v to your command to get extra info printed while processing is happening. Is there an error reported earlier in the log? Are you running this on a machine with 100 cpus? It is likely that an earlier step crashed and qsiprep failed to exit

I didn’t see the HTML files in the qsirecon directory. This is weird.

Thanks. I will add -v to my command.

In the logs directory, I only found the CITATION files but not other files.