Qsirecon missing figures for report

Software Support
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Summary of what happened:

Dear group,
Perhaps I do not understand the consequences of some of these flags!
I ran qsirecon, and it produced the expected reconstructions and reported no errors. However, the figures directory is empty and the report is pretty sad looking without any figures.

Does this: --skip-odf-reports --recon-only prevent the creation of the report figures entirely?

I tried running with the --reports_only flag, but the figures directory remains empty.

Thank you for your insights.

Command used

export SIF=/contrib/singularity/shared/neuroimaging
export MRIS=/groups/dkp/Batch/CAM003_bids_data

Subject=${sub}

singularity run --cleanenv --bind ${MRIS}/data:/data:ro \
--bind ${MRIS}/derivatives2/qsiprep:/qsiprep-output:ro \
--bind ${MRIS}/derivatives2:/out  \
--bind ${MRIS}/qsi_work3:/work \
${SIF}/qsiprep.sif /data /out participant \
--participant_label ${Subject} \
--recon-input /qsiprep-output \
--recon-spec mrtrix_multishell_msmt_ACT-hsvs \
--stop-on-first-crash \
--output-resolution 1.3 -w /work -v -v  \
--n-cpus 16 --omp-nthreads 15 \
--skip-odf-reports --recon-only \
--fs-license-file ${HOME}/license.txt \
--freesurfer_input /out/fmriprep2301/sourcedata/freesurfer

Version:

qsiprep 0.16.1
(also tried with qsiprep 0.17.0)

I also tried several reconstruction algorithms. None produce figures in the derivatives/qsirecon directory

Environment (Docker, Singularity, custom installation):

Apptainer running on HPC cluster

Data formatted according to a validatable standard? Please provide the output of the validator:

This is a BIDS-validated dataset used for testing.

2

Hi @Dianne_Patterson,

--recon-only means only do reconstruction (i.e., postprocessing). --skip-odf-reports means to skip generating the pictures of the orientation distribution functions for the reports. This was added since a lot of HPC systems had trouble with the graphics generations, so it goes… The reconstruction HTML reports are not (yet) as thorough as preprocessing, so those ODF reports are the main figures that would be in there. So by skipping them, your html reports are shorter.

That being said, you can open the WM FOD image in mrview to do you own quality assurance.

--reports-only will just only create the HTML reports and is meant to be run if you have a working directory of a complete run somewhere and you just accidentally deleted the html report.

Best,
Steven

1 Like
3

Thank you so much for your clear explanations! I really appreciate it. I had not realized that HPC systems in particular had trouble generating the reports. I also appreciate your suggestion to use mrview to display the FOD. I’m still getting used to the terminology and concepts.

1 Like
4

Has there been much success with changing the rendering backend in QSIPrep for HPC usage?

For some of our internal data visualization projects that use singularity containers, we were able to reliably render plots by switching the matplotlib backend to tkagg (Backends — Matplotlib 3.7.1 documentation). Perhaps there could be a command line argument for QSIPrep to toggle a common & reliable backend on HPC systems?

5

Our matplotlib figures are coming out fine, it’s the vtk/opengl used in FURY that have been hit or miss on HPCs.